ABC News' Shushannah Walshe and Barbara Schmitt report:

HATTIESBURG, Miss. - In a nail biter of a race, six-term incumbent Thad Cochran has defeated his tea party challenger State Sen. Chris McDaniel in the Mississippi GOP Senate primary run-off. With 98.1 percent percent of the vote in, Cochran bested McDaniel 50.7 percent to 49.3 percent, a difference of less than 4,800 votes, according to The Associated Press.

McDaniel failed to concede or congratulate his opponent Tuesday in a speech to about 200 supporters at the Hattiesburg Lake Terrace Convention Center.

"It's our job to make sure that the sanctity of the vote is upheld," he said. "Before this race ends, we have to be absolutely certain that the Republican primary was won by Republican voters."

This was a re-match for the two, as neither reached the 50 percent threshold on their primary day earlier this month.

In that race it was actually McDaniel who came out on top, besting Cochran, 76, by 1,400 votes. In a rare situation for a run-off, voter turn-out was up significantly Tuesday. Three weeks ago, 313,483 votes were cast between Cochran, McDaniel and a third candidate. On Tuesday, more than 360,000 votes were cast.

Run-offs are traditionally difficult for incumbents, but Cochran had a huge fundraising advantage and had been reaching out to traditionally Democratic constituencies in the weeks since the primary.

The Cochran campaign was openly courting African-American voters, who are traditionally Democrats. The McDaniel campaign blasted Cochran for the strategy, since it is a GOP primary, but is perfectly legal in the state. The primary is an open one, so any Democrat who did not vote in the Democratic primary earlier this month would be free to vote today. Legally, a voter casting a ballot today must have the intent to vote for the same candidate in the general election, something impossible to enforce.

In Hattiesburg at the convention center where McDaniel and his supporters were celebrating just three weeks ago, about 200 supporters watched the results trickle in on the monitors. Instead of the joy they expressed earlier this month, they were holding their breath and clenching their hands as the results came in throughout the night.

The primary was dubbed the "dirtiest" and " nastiest" this cycle, with the run-off no different and both sides going at each other until the very end.

Mississippi Republican Party chairman Joe Nosef said he is "very disappointed" about how nasty the race became, saying it will only hurt the party in the general election.

"I've been saying for months, this is the exact thing we didn't need to happen," Nosef said. "What made it worse, I think, is it just seemed more personal than it would normally be, than it needed it to be and for me the thing that upset me the most is we didn't just have the candidates attacking themselves, we had candidates attacking the party."

Nosef added: "We are going to have to overcome this and I am confident we will, but it will take more time and more gray hair than it originally would have."

In an interview with ABC News before the results came in, former Senate majority leader and fellow Mississippian Trent Lott, who vigorously backed Cochran, said he hoped Cochran would "get reelected for the good of the state and the country."

"I'm sorry the primary has been as ugly as it has been, it's not the way it usually is in Mississippi," said Lott, who cut an ad for Cochran during the run-off.

The run-off remained just as ugly in the final days.

Cochran ran an ad titled "Own Words," detailing the many eyebrow-raising comments McDaniel made during his time as a radio talk show host, including saying a female candidate was "using her breasts to run for office" and calling a Hispanic woman, "mamasita."

In an interview after the primary, former Mississippi Gov. Haley Barbour - who supported the pro-Cochran superpac - said there would be no backing down in these extra weeks, telling ABC News: "We are not going to let a bunch of people from Washington or New York dictate who represents Mississippi in the U.S. Senate."

Barbour was referring to the large amount of out of state money and help McDaniel got in his campaign from outside tea party groups.

In a brief interview this evening as the results trickled in, Barbour said he thought the Cochran camp ran a "far better" campaign in the run-off than the primary. He said the "issues" were able to "come into play more," while during the primary they were "smothered by all the nastiness," which he also believes helped benefit Cochran.

Barbour added he thinks the issue of education helped Cochran, calling it the "biggest contributor" if he were to win.

In April, McDaniel said the federal government should have no role in education, including paying for it, but it wasn't until the run-off that Cochran supporters began to hammer McDaniel for the comment.

If McDaniel had won, Democrats would likely have used Cochran's playbook to boost their candidate, former Rep. Travis Childers, but even with Cochran's win, Nosef said they will still have a competitive general election on their hands.

"I think this campaign has been so unfortunately brutal and personal that the general election is going to require more work," Nosef noted. "I am assuming we will absolutely have a race … as our race has gotten dirtier, they seem to have gotten emboldened unfortunately. I expect us to win because I think Mississippi doesn't need to send Travis Childers to the Senate, but I think it's going to be a tougher race and require more work."

Cochran, known as "Gentleman Thad," was elected to the House in 1972, serving three terms before being elected to the Senate.

Conservative notables, including Sarah Palin, Rick Santorum, and even longtime game show host Chuck Woolery, have been stumping for McDaniel, all joining his call that Cochran is out of touch, embodies Washington, D.C., and that his time is over.

John McCain made a last-minute visit for Cochran and Mississippi native Bret Favre starred in a Chamber of Commerce-funded ad in which he said "Thad Cochran always delivers, just like he did during Katrina."

Cochran's message throughout the campaign was that he's the choice that can bring in those federal dollars and disaster relief money, something McDaniel's supporters called nothing more than pork.

Cochran has enjoyed healthy fundraising directly to his campaign - $1.15 million since June 4 - more than half of it coming from political action committees. He's also enjoyed solid outside spending on his behalf, as a coalition led by the National Rifle Association and highlighted by the National Association of Realtors, and the Barbour-backed superpac Mississippi Conservatives, has spent $2.23 million to support him and attack McDaniel.

A broad array of agricultural interests, large corporations, and some fellow GOP lawmakers, including Senate Minority Leader Mitch McConnell and a few other senate colleagues, have also pitched in to help Cochran.

McDaniel's effort was funded almost entirely by outside spending: His campaign raised only $174,900 since June 4, but outside groups have combined to inject over $2 million into the race. The Club for Growth led the way, with Tea Party Patriots, Independent Women's Voice, and FreedomWorks chipping in, among others.

FreedomWorks alone said they had more than 100 "Get Out the Vote" events in the 36 hours before the run-off. They added their activists knocked on more than 140,000 doors, put up more than 60,000 yard signs, and they believe they reached hundreds of thousands of Republicans in the state through an online campaign.

Along with the nastiness, the campaign had its low and odd points.

In April, a McDaniel supporter sneaked into a nursing home where Cochran's bedridden wife has lived for more than a decade with dementia. Once inside, the McDaniel supporter proceeded to secretly film the wife of the three-term congressman-turned-senator and then put the video online. McDaniel disavowed the act and says he has no relationship with the conservative blogger. Four people were arrested and although it grabbed headlines, the issue faded as the primary turned into a run-off.

During the run-off, questions arose about Cochran's clarity when he seemed to not know about Eric Cantor's stunning primary loss, despite talking publicly about the defeat previously. It didn't matter in the end, though, as he came back from what looked like political death to beat McDaniel.

ABC News' Christopher Good and Ben Siegel contributed to this report.

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(Rogelio V. Solis/AP Photo)