Sanford's loss writes another bizarre chapter in a political career full of controversy and distraction.
Forced into political exile after lying about an extra-marital affair he was having while Governor of South Carolina, Sanford made an unexpected comeback in 2011. He won the Charleston-based congressional seat in a special election, and established himself as a fiscally conservative, libertarian-leaning voice and member of the House Freedom Caucus.
The loss makes Sanford the second House member to lose a primary this cycle after Rep. Robert Pittenger, R-N.C. was defeated last month by pastor Mark Harris.
Sanford is also not alone in facing backlash as a Republican willing to voice his criticism of President Trump. Last week, Alabama GOP Rep. Martha Roby was forced into a runoff election after a primary contest that centered on her decision to not vote for Trump following the October 2016 publication of his vulgar comments during a filming of "Access Hollywood."
The result further solidifies the trend for Trump critics in the Republican Party, and comes on the heels of the decisions by GOP Senators Jeff Flake and Bob Corker – both prominent Trump critics – to not seek re-election this cycle.
"Certainly we’ve seen some problems in primaries for Trump critics in the party," said Kyle Kondik, an analyst at the University of Virginia Center for Politics, "Being a Trump critic is a hard position to be in in the Republican Party, and I don’t think Sanford’s sometimes criticism of Trump helped him, that’s for sure."
Despite the effect that Trump may or may not have had on the race, Kondik also pointed out that Sanford, who garnered just 56 percent of the vote in the 2016 Republican primary in his district against a little-known challenger, was already a prime candidate to become one of the handful of members who fall victim to primary challengers each election cycle.
"Sanford's performances in the past have been weak," Kondik said, "Very rarely do House members lose re-nomination and Sanford but a logical candidate given his opposition to Trump and his general weakness with the electorate."
Sanford is indeed an outspoken challenger of Trump, but his defiance of the president may have contributed to his upset defeat.
During the 2016 presidential election, after Trump ventured to Capitol Hill to meet with Republicans, Sanford came out of the meeting telling reporters, "I wasn’t particularly impressed."
"It was the normal stream of consciousness that’s long on hyperbole and short on facts," he added.
He also thrusted some blame onto Trump for increasing divides within the modern Republican party and creating an even more volatile political climate.
"I would argue that the President is at least in partially – again not in any way totally, but partially to blame for demons that have been unleashed," Sanford said in a June 2017 interview with MSNBC.
Aboard Air Force One, Trump endorsed Sanford’s opponent mere hours before polls closed, tweeting, "Mark Sanford has been very unhelpful to me in my campaign to MAGA. He is MIA and nothing but trouble."
Mark Sanford has been very unhelpful to me in my campaign to MAGA. He is MIA and nothing but trouble. He is better off in Argentina. I fully endorse Katie Arrington for Congress in SC, a state I love. She is tough on crime and will continue our fight to lower taxes. VOTE Katie! — Donald J. Trump (@realDonaldTrump) June 12, 2018
My political representatives didn’t want me to get involved in the Mark Sanford primary thinking that Sanford would easily win - but with a few hours left I felt that Katie was such a good candidate, and Sanford was so bad, I had to give it a shot. Congrats to Katie Arrington! — Donald J. Trump (@realDonaldTrump) June 13, 2018
The stunning upset also drew reaction from across the political world, as the news reverberated around an already unsettled political landscape ahead of the 2018 midterm elections in November.
Former Rep. Reid Ribble, R-Wis., expressed outrage at Sanford’s loss, noting that the South Carolina congressman "supported POTUS with his votes" on issues from taxes to healthcare to government spending.
"Yet because he was willing to honor Article 1 Separation of Powers and speak his mind, he loses a primary? We have entered the twilight zone…," Ribble tweeted Wednesday morning.
Sanford took his loss in stride during his first ever concession speech in Mount Pleasant late Tuesday night.
"It may have cost me an election, but I stand by every one of those decisions to disagree with the president because I didn't think they would be concurrent with the promises I made when I first ran for office and for the very voices of the people of the 1st District that I represent,” he said, according to the Post and Courier.
Her unexpected victory now makes Arrington the poster child for the pro-Trump wing of the Republican Party's 2018 takeover.
In her victory speech Tuesday night, Arrington embraced the president wholeheartedly and implored the party to stand by him.
"We are the party of President Donald J. Trump," she said.
In Virginia, Corey Stewart, known for courting controversy and a figure who faced criticism for his response to the violence in Charlottesville, won the GOP primary for U.S. Senate in another result that showcased the sway proving one's loyalty to President Trump can have on Republican voters.
Stewart narrowly edged out State Delegate Nick Freitas and earned praise from the President on Twitter this morning.
ABC News' Meena Venkataramanan contributed to this story.