The wedding took place Friday at Capella Church in the Grand Del Mar Hotel in San Diego, E! Online reported.
"It was beautiful," an eyewitness told E! News. "They had cocktails on the lawn right after. Everyone seemed really happy."
Prejean, 23, and Boller, 29, have been a couple for a year and announced their engagement in February.
A native of San Diego, Prejean was raised in Vista, Calif., as an Evangelical Christian. She won the Miss California USA competition in 2009 and became first runner-up in the Miss USA contest.
But it was her answer to a judge's question that made her famous when she said she believes marriage should be between a man and a woman. She later wrote a book, "Still Standing: My Fight Against Gossip, Hate and Political Attacks."