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.

The Ralph Lauren outfit was in keeping with the theme of this year's ball, an homage to Japanese designer Rei Kawakubo, and won fashion plaudits from the moment she glided up the stairs.
There have been close to 16,000 tweets just about Chopra, which means the country has been tweeting about her pretty much since waking up.
... is it really an advertisement for Indian Prime Minister Narendra Modi's pet "clean India" movement, locally known as Swacch Bharat Abhiyan? Because obviously the dress would be a highly effective cleaning mechanism.
This seems to be by far the most popular theory around her dress and what it means. Some people have even tweeted directly to the prime minister, asking him to appoint her as an official "ambassador" for the project.
The movement has used celebrities including cricket legend Sachin Tendulkar and Bollywood superstar Amitabh Bachchan as ambassadors before, so as theories go it isn't too far off!
We're just going to let this tweet speak for itself.
The verdict in both India and the US is near unanimous - Priyanka Chopra simply won in that dress.
Elle Magazine called the dress "FANCY", US Magazine declared that "Priyanka Chopra slayed"  and Time Out New York picked her as one of its 10 best "favourite looks" at the Met Gala.
In pictures: Met Gala's oddest outfits
The press reactions in India have run along similar lines. The Times of India newspaper said that she "swept away the competition" while the Deccan Chronicle said she "looked like a princess".
The sentiment on Twitter was not too far off.
Some reports say  that this is the world's longest trench coat - and with material like that up for grabs, it's an opportunity too good for any photoshop enthusiast worth his/her salt. It is unclear at time of writing if Guinness World Records have been contacted.
Britain's Jonathan Rea overcame wet conditions in Germany to secure victory and move 47 points clear in the World Superbike Championship standings.
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The Met Gala usually draws little interest in India, but this year actress Priyanka Chopra's appearance in a vast detective trench coat outfit has inspired jokes, memes and even profound symbolic interpretations.