Rea was unable to match the speed of his Ducati rival on the long start/finish straight, but the six-time champion closed onto Bautista’s rear wheel on the last lap and made his move to hit the front at Turn 7.
However, the Spaniard was back in front again as they powered away from the exit, but Rea went underneath the Ducati rider at the chicane in what proved to be a race-winning pass.
The Northern Ireland man had a big moment through the final corner as Rea put the power down hard on his Kawasaki, wary of being out-dragged to the line by Bautista.
He managed to hold on and crossed the line for his second win of the weekend after winning the earlier Superpole race, with Bautista 0.194s back.
It was Rea’s 117th career victory in World Superbikes and the 35-year-old is now 17 points behind Bautista after the first three rounds of the championship, reducing the 37-year-old’s advantage by a single point after Bautista held an 18-point lead going into the weekend.
Reigning champion Toprak Razgatlioglu faded in the closing stages and had to settle for third, with the 25-year-old yet to win a race this season.
The Turkish rider is 52 points behind Bautista and 35 behind Rea.
Alex Lowes finished fourth (Kawasaki Racing) ahead of Andrea Locatelli on the Pata Yamaha, with Iker Lecuona sixth (Honda).
Eugene Laverty was 14th on the Bonovo Action BMW after crashing out of the Superpole race. Scott Redding was the leading BMW rider in 11th.
Round four of the championship takes place at Misano from June 10-12.