For her part, Clinton largely resisted commenting on the controversy, although she did call Wright's remarks "offensive and outrageous."
But, privately, many Clinton aides admitted they were hearing from superdelegates concerned about Wright's controversial remarks.
During that same time, Clinton also faced controversy surrounding an exaggerated description she gave of a 1996 trip to Bosnia.
Clinton said she and her crew landed in an "evasive maneuver under sniper fire," describing her trip to Tuzla as if it were a scene from "Saving Private Ryan."
"There was supposed to be some sort of greeting ceremony, but instead we just ran with our heads down to get into the vehicles," she said.
Questions surrounding whether Clinton had embellished the story were particularly embarrassing for her because a central theme to her campaign had been her "experience," arguing that she is ready to answer the 3 a.m. crisis call at the White House.
Video footage contradicted Clinton's account, revealing no visible threat in Tuzla and a brief greeting ceremony on the tarmac there.
Clinton later said she "misspoke" when describing the account.
And on the heels of the Wright controversy, Obama came under fire for remarks perceived as insulting to small town voters, like many in rural Pennsylvania.
"It's not surprising, then, they get bitter, they cling to guns or religion or antipathy to people who aren't like them or anti-immigrant sentiment or anti-trade sentiment as a way to explain their frustrations," Obama told a crowd at a San Francisco fundraiser.
The comments, first posted on The Huffington Post, opened a line of attack against Obama that he was too elitist or out of touch to connect with the white, working class voters who had been flocking to Clinton in recent contests and would be key in battleground Pennsylvania.
Both incidents -- and reaction to the Wright controversy -- played a prominent role when the candidates met for the final time on a debate stage in Philadelphia.
After a six-week stretch between contests, Clinton decisively won the Keystone State by nearly a 10-point margin.
"Some people counted me out and said to drop out, but the American people don't quit, and they deserve a president who doesn't quit, either," Clinton told supporters at a victory rally in Philadelphia.
The day after her win, Clinton told Diane Sawyer on "Good Morning America" that the win should send a message to unpledged superdelegates.
"The road to the White House does go through Pennsylvania," she said, adding that the Pennsylvania win proved that she can win the large and swing states considered crucial to a November victory.
Flanked by her husband and daughter, Clinton thanked Indiana voters for their support, but she was not the relentlessly upbeat Clinton of victories past. And in contrast to other primary night parties, Bill Clinton stood unsmiling behind her for much of the speech.
Clinton pledged to "never stop fighting for you," but faced with a decisive Obama victory in North Carolina and uncertain results in Indiana, she also seemed to concede the possibility that she might not become the eventual nominee.