Taking advantage of a "balance of performance" adjustment by sanctioning body IMSA that lessened horsepower capabilities for the Daytona Prorotypes, Van Overbeek edged Jordan Taylor by 5.833 seconds in the caution-free, two-hour race, completing 87 laps in Extreme Speed Motorsports' No. 2 Honda-powered HPD ARX-03b.
Van Overbeek passed Taylor with 15 minutes left on the 11-turn, 2.238-mile road course.
Taylor teamed with brother Ricky in the Corvette DP. Memo Rojas and Scott Pruett were third in the No. 01 Ford EcoBoost/Riley DP.
Jan Magnussen and Antonio Garcia raced to their second straight GT Le Mans class victory and finished eighth overall. They completed 84 laps in the No. 3 Chevrolet Corvette C7.R.
Earlier, in the Prototype Challenge and GT Daytona event, Mirco Schultis and Renger van der Zande won the Prototype Challenge class in Starworks' No. 8 ORECA FLM09.
Schultis and van der Zande completed 82 laps in the two-hour race, finishing 12.234 seconds in front of the No. 25 8Star Motorsports ORECA FLM09 driven by Sean Rayhall and Luis Diaz.
Markus Palttala and Dane Cameron took the GT Daytona division in the 94 Turner Motorsport BMW Z4 after leader Spencer Pumpelly's Audi R8 LMS ran out of fuel on the final lap.
Palttala and Cameron ran 78 laps.