Trailing 66-64 with 17.1 seconds left in regulation, Arkansas forward Alandise Harris missed the front end of a 1-and-1 and Wilbekin followed by banking a shot off the backboard for a tie.
In the ensuing overtime, the Gators' Patric Young began by making a jumper, and Wilbekin then forced a steal and finished the play with a 3-pointer for five-point lead.
Florida's Dorian Finney-Smith (22 points, 15 rebounds) netted six straight points, but the Razorbacks answered with a 6-1 run, shaving their deficit to three with 42 seconds left.
Wilbekin, however, drained 6-of-8 free throws in the closing seconds to secure the win for the Gators (13-2, 2-0 SEC), who snapped Arkansas' 23-game home win streak despite the absence of leading scorer Casey Prather (knee).
Wilbekin ended with 18 points.
Rashad Madden provided 23 points and Coty Clarke added 16 with 14 rebounds for the Razorbacks (11-4, 0-2).