The Gators had a 45-33 lead with 12:50 remaining after Murphy hit a pair of free throws, but Alabama responded with a 16-4 run to tie it at 49 on JaMychal Green's three-point play with 6:52 to go.
Alabama had a chance to tie in the final seconds, but Trevor Lacey's 3-pointer bounced off the front of the rim.
Florida (23-9) snapped a three-game slide and will face top-ranked Kentucky on Saturday in the semifinals.
Alabama (21-11) lost for just the second time in seven games. Green had 22 points, Trevor Releford scored 12 and Lacey added 11.
It's been a struggle of late for Florida, which lost its last three regular-season games to Georgia, Vanderbilt and Kentucky.
And this one wasn't much different — except for the final result. The Gators shot just 32 percent (8 of 25) from the field in the first half and led 26-24 at the break after Alabama's Levi Randolph hit a long 3-pointer at the buzzer.
Alabama's defense had something to do with Florida's offensive woes. The Crimson Tide's bruising, grind-it-out style is completely opposite of the Gators, who like to run, shoot and turn the game into a constant sprint.
It wasn't until Erving Walker's outburst early in the second half that the Gators were finally able to get some separation. The 5-foot-8 point guard scored seven points in less than five minutes, shrugging off Alabama's physical guards and consistently getting into the lane, where he could finish at the rim or find another shooter around the 3-point line.
For a while, it looked as if the Gators looked would cruise, but Alabama erased a 12-point deficit in less than six minutes. The Tide got a huge game from Green, who was 7 for 14 from the field and 8 of 9 from the free-throw line. He also grabbed 10 rebounds and dished out four assists.
But that one miss at the free-throw line hurt.
Green had a chance to tie it with 20.3 seconds remaining, but his second of two foul shots rattled out and Kenny Boynton converted both of his free throws on the other end to push Florida's lead to 66-63. Boynton finished with 14 points.
Lacey got a fairly clean look on the last-gasp 3-point attempt, but it was short, clanging off the front of the rim. The Tide shot 56.5 percent from the field (13 of 23) in the second half and outrebounded Florida 32-27 for the game.
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