Miss Oklahoma, Olivia Jordan, took top honors at the contest, which is co-owned by Trump and came under fire after his controversial claim that Mexico was sending criminals to the United States.
Broadcaster NBC and Spanish-language Univision both said they would not air the show and a co-host pulled out, but the pageant went forward and included numerous contestants with ties to Mexico.
While the question of immigration and Trump's comments never came up on stage, the competitors nonetheless faced questions on topical issues.
For one of her winning questions, Jordan said race relations is the number one issue America still needs to tackle.
"We really need to work on being an accepting society, and being a society where every single person -no matter your race, no matter your gender - is given the same rights and privileges and opportunities," the model said at the show in Baton Rouge, Louisiana.
Women with careers ranging from modeling to law strutted in bikinis and gowns, and answered questions as the glamorous squad was whittled down to one.
Miss USA aired on the cable channel Reelz after NBC and Univision cut ties with Trump.
The billionaire business magnate sparked a firestorm over his comments, saying Mexico was "sending people that have lots of problems... They're bringing drugs. They're bringing crime. They're rapists."
"When Mexico sends its people, they're not sending their best," the Republican White House hopeful said on June 16.
Trump did not attend the pageant, tweeting that he was busy campaigning in Arizona.
Several companies and countries have decried Trump over the comments.
Costa Rica pulled out of the Miss Universe competition following the remarks, and said they would not be sending their contestant to the international pageant.
But Trump's voluble and unfiltered style has won him a surge of support amid a chaotic Republican field with few frontrunners.
While the mogul's business interests have taken a hit, his political profile has soared. He is polling as the number two contender in the party's showdown for the 2016 election.
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