Florida State (19-8, 9-7 Atlantic Coast Conference) scored its final eight points from the free-throw line, including five from Thornton, as the Seminoles took control after trailing Miami (15-14, 7-9) for much of the second half.
Thornton's final two free throws gave the Seminoles a 66-61 lead with eight seconds remaining.
Miami's Guillermo Diaz hit a 3-pointer to pull the Hurricanes within two 5 seconds later, but Florida State sealed the win when Todd Galloway converted 1-of-2 free throws with 2.6 seconds left.
Robert Hite's 80-foot desperation shot caught the back of the rim but failed to fall for Miami. Hite scored a game-high 20 points for the Hurricanes.
It was the first win in four games against Miami for Florida State, which greatly helped its cause for an NCAA Tournament bid by winning four of its final five games. The Seminoles upset then-No. 1 Duke, 79-74, on Wednesday behind 26 points from Thornton.
Miami's loss means its push for a tournament bid likely fell short.
The two teams traded leads before Miami went up 61-59 on a basket by Diaz, who scored 16 points, with 1:57 remaining. But the Hurricanes missed four of their final five shots, while the Seminoles converted 10 of 12 free throws down the stretch.
Alexander Johnson had 14 points and 10 rebounds for the Seminoles, who outrebounded the Hurricanes 35-27 and shot 50 percent (5-for-10) on 3-pointers.
Miami scored 15 of the first 18 points of the second half, taking a 45-38 lead on a 3-pointer by Hite with 12:29 remaining in the game.
But Florida State responded by forging a 50-50 tie on a 3-pointer by Galloway at 8:08. The Seminoles regained the lead, going up 55-54 on a free throw by Jason Rich at 6:05. Hite had another 3-pointer to put the Hurricanes up 57-55 at 5:50.
Miami honored its four seniors, including Hite, before their final regular season game.
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