The Gators (9-2) led 83-80 in the closing seconds before Calathes drained a 3-pointer. He scored 10 of Florida's final 19 points.
Antonio Hanson led the Eagles (3-6) with 16 points and five assists.
The Gators were up 58-42 early in the second half, but the Eagles used a barrage of free throws to get back in it. Consecutive 3-pointers from Colby Wohlleb and Trumaine Pearson made it 71-66 with a little more than six minutes remaining.
Sandy Perry's three-point play with 38.6 seconds left cut Florida's lead to 83-80. Then Calathes hit his long-range shot to seal the win.