The reigning champion from Northern Ireland led from early in race two and won by nine seconds.
Rea's main title challenger and Kawasaki team-mate Tom Sykes slipped off but recovered to finish 12th.
Alex de Angelis was second and Xavi Fores third, with Welshman Chaz Davies, who won Saturday's opener, sixth.
Heavy rain at the Lausitzring circuit led to the start being delayed twice on Sunday.
Yorkshireman Sykes, who cut the gap on Rea to 26 points with Saturday's win, moved in front on the first lap.
However, he was quickly replaced by Rea before skidding off and ending his hopes of victory.
Sykes was able to continue but from the back of the field and he moved through to take four points.
Rea was never threatened as he secured a much-needed 25 points after failing to finish the last two races.
The riders have three rounds remaining in France, Spain and Qatar.
Britain's Jonathan Rea overcame wet conditions in Germany to secure victory and move 47 points clear in the World Superbike Championship standings.