It was neck-and-neck between Loris Baz (Ken Tate Racing Yamaha) and Rea for large portions of the race.
With eight laps left, Michael van der Mark (Pata Yamaha WorldSBK Official Team) surged into second before Baz drifted off the track and did make a good recovery before slipping down into fourth.
Moments later Lowes moved into the front pack with one-and-a-half seconds separating the first nine riders.
And with five laps left, Rea registered his quickest lap to pull into the lead. Van der Mark sensed he had to attack and reduced the gap to the Northern Irishman.
Race 1 winner Toprak Razgatlioglu (Yamaha WorldSBK Official Team) and Bas made contact in lap 20 which forced the Turk to withdraw while Lowes was able to get ahead of Rea and pull away.
And in a thoroughly entertaining final lap with Rea and Lowes neck-and-neck, it was the latter who emerged victorious to win with his new team for the first time.
LOWES: I WAS GETTING FRUSTRATED
"Honestly the race was tough," Lowes said after the race.
"I didn't get off to the best of starts. Jonathan was trying to control the pace which was quite slow and everyone was banging in to me. I had a little collision with Toprak and Michael hit me so I kept dropping back and I was getting frustrated.
"But I knew my pace was good and I wanted to be in a position to fight at the end. Luckily it fell quite good for me.
"My bike was really fast so I could pass people on the straight. I really enjoyed it. It was a slippy race.
"The lap times weren't fast but it was fantastic."
REA WON THE SUPERPOLE
Rea wins the Superpole race by the finest of margins!
Rea bounced back from his crash in Race 1 to win the Superpole race in dramatic fashion as he pipped Toprak and Redding.
LOCATELLI DOMINATES ON WORLDSSP DEBUT
Rookie Locatelli dominant on his WorldSSP debut
Italian rookie Andrea Locatelli (BARDAHL Evan Bros. WorldSSP Team) won the first Supersport World Championship race of 2020 with reigning champion Randy Krummenacher failing to complete a turn as he crashed out.