Virginia won the College Cup when Riggs Lennon slipped a low shot past diving goalkeeper Earl Edwards Jr. in the fifth round.
The Cavaliers (14-6-3) won their seventh national title and first since 2009.
"As disappointing as it was to have lost, I think most people would say today we were the better team," UCLA Coach Jorge Salcedo said. "Ultimately, we didn't find a way to score a goal, and that was our demise."
The Bruins had the best scoring opportunity in overtime in the 96th minute. Abu Danladi's one-hop shot after a deflection in the penalty area was saved by goalkeeper Calle Brown, the tournament's most valuable defensive player.
UCLA's best chance in regulation came in the 54th minute on a header by Larry Ndjock. Felix Vobejda sent a cross from the right of the penalty area that was deflected over to Ndjock, whose header missed wide left.
"It's easy for me to delve into the negative tactics, but it is what it is," Salcedo said. "It was very difficult to break down. There's a saying in soccer that sometimes teams park a bus in front of their own goal. I feel like today there were two buses in front of the goal."
Virginia led, 2-1, after three rounds of penalty kicks with UCLA's Gage Zerboni and Willie Raygoza missing on blasts off the crossbar.
Patrick Foss of Virginia and Ndjock converted to set the stage for Lennon's left-footed winner.
"I couldn't believe it," Lennon said. "I just turned around and saw everyone running at me. I saw the crowd going nuts, and I was like, 'We just won a national championship.' It's the best feeling I've ever had."
Edwards made three saves for UCLA (14-5-5), which had scored three goals in each of its last three games.
Virginia's victory came 17 years to the day of the last time it met UCLA in the NCAA final, a 2-0 victory by the Bruins.
Virginia packed in its defense for much of the game, content to let the Bruins handle the ball in the midfield while preventing any free runs to the goal.
The strategy helped create a huge advantage in possession for UCLA, but the Bruins struggled to produce serious scoring threats despite outshooting the Cavaliers, 15-9.
The Cavaliers were in the College Cup for the 12th time, including the second year in a row. UCLA was seeking its fifth national championship in its 14th trip to the final four.