Jermaine Beal chipped in 13 points for the Commodores, including two key free throws with 6.2 seconds remaining.
Vanderbilt (23-6, 12-3 Southeastern Conference) swept the season series for the first time since 1997 and stayed in the hunt for the league's regular-season title. The Commodores need No. 3 Kentucky to lose its remaining two games to have a chance.
Vernon Macklin led the Gators (20-10, 9-6) with 21 points and nine rebounds. No other Florida player scored in double digits, the biggest problem for a team trying to get back to the NCAA tournament for the first time in three years.
Nonetheless, coach Billy Donovan's team had several chances to pull off an upset. But Macklin missed a free throw, Erving Walker missed a short jumper and Kenny Boynton missed a 3-pointer with 10 seconds remaining.
The Gators even tipped in the go-ahead basket. Dan Werner, the team's lone senior who was recognized before his final home game, tipped one through Vandy's hoop with 1:06 to play.
Werner somewhat made amends with a blocked shot on Vandy's next possession, but Florida struggled down the stretch and lost for the fourth time in its last seven games.
The Gators have dropped two straight and play the Wildcats in the regular-season finale Sunday.
Florida turned the game with a 16-2 run midway through the second half, and Boynton did most of the work.
Erik Murphy had a tip-in, then Boynton found Alex Tyus and Macklin for layups on consecutive trips. Macklin followed with a one-handed jam off Boynton's miss, and then Boynton tipped in a shot to give the Gators their first lead of the game.
Jeffrey Taylor silenced the O'Connell Center with a dunk on the other end, but Florida kept it going when Tyus hit a short jumper and Macklin got loose for a layup that made it 53-48 with 9:24 remaining.
The Commodores got it back to 55-54 on Jenkins' 3 from the corner, Vandy's eighth of the game. Jenkins hit another one about a minute later — his fifth — and tied it at 57.
Florida had it tied again, 60-all, and Ogilvy got credit for the basket that Werner tipped home.
Vanderbilt opened a 12-point lead midway through the first half — thanks mostly to four early 3-pointers — but Florida used a late surge from some unlikely sources to cut it to 38-35 at halftime.
Macklin, who had just two points in the first meeting in early January, hit four consecutive baskets to get it close. He finished the half with 12 points.
Ray Shipman, a seldom-used guard, was even more surprising in the final minute. Shipman hit a jumper with 50.7 seconds remaining, then made a 3-pointer at the buzzer. His first 3 since Nov. 27 against Michigan State helped Florida close the first half on a 10-3 run.
Shipman, who entered the game averaging 2.4 points, had missed 12 of 14 shots from behind the arc this season.