The Pata Honda rider broke clear on lap seven of a race that was reduced by one lap to 17 due to heavy rainfall.
Eugene Laverty (Aprilia Racing) edged out Crescent Suzuki Team's Leon Camier for second place during a tight final lap.
Laverty's team-mate Sylvain Guintoli, the championship leader, finished fourth.
"I was starting to get frustrated with the problems I was having, but now I've kept up my record of winning a race in every year of my career," Rea said.
"I used my head, tried to be smart and didn't make any mistakes.
"I'm so happy and my team deserves that victory."
The poor weather also affected the day's second race, which was won by Kawasaki's Loris Baz after the red flag came out on the final lap with conditions rapidly deteriorating.
Baz, who also won at the Northamptonshire track last year, finished ahead of compatriot Jules Cluzel, the Suzuki rider taking his maiden podium despite falling at Stowe before the race was stopped.
Laverty took the final podium place, while Guintoli stretched his lead at the top of the standings to 13 points after finishing sixth, one place ahead of nearest challenger Tom Sykes (Kawasaki), who earlier could only manage 11th in race one.