Bautista inherited pole position for the short-distance race when Rea was relegated to the back of the grid after hitting Alex Lowes at the last corner in Saturday’s Race 1.
He kept the lead off the line and led all 10 laps of the race, comfortably winning by 2.7 seconds.
GRT Yamaha’s Marco Melandri spent most of the race in second, first leading Leon Haslam and Tom Sykes before Michael van der Mark and Lowes started to gain ground.
Lowes ended up crashing out at Turn 7, failing to score for the second race in a row, but his Yamaha teammate van der Mark passed both Sykes and Haslam before attacking Melandri.
Van der Mark finally took second with three laps remaining at Turn 6 to repeat his Race 1 result, with Melandri completing the podium.
Rea, after gaining eight positions on the opening lap to run 10th, quickly passed Chaz Davies, benefited from Toprak Razgatlioglu and Jordi Torres both going wide and overtook Sykes and Haslam to move up to fourth by the halfway point of the race.
However, from then on, he couldn’t close in on the Yamahas of Melandri and van der Mark and settled for fourth.
BMW rider Sykes beat Haslam to fifth with two more Kawasakis, Razgatlioglu (Puccetti) and Torres (Pedercini) completing the top eight.
Sandro Cortese (GRT Yamaha) finished ninth followed by three Ducatis: Chaz Davies, Michael Ruben Rinaldi (Barni) and Tommy Bridewell (GoEleven).
Loris Baz (Ten Kate Yamaha) was unable to start the race.