Degenkolb was one of six Giant-Alpecin riders who were hit by a car on a training ride in Calpe, Spain, in January. He nearly lost a finger in the incident, and only returned to racing in April.
The injury and loss of training meant that Degenkolb could not defend his 2015 Milan-San Remo and Paris-Roubaix titles.
The 27-year-old German sprinted ahead of Belgian Roy Jans (Wanty-Groupe Gobert) to take the Münsterland Giro victory. The race is ranked 1.HC by the UCI, and runs over 214 kilometres.
“There was perfect team spirit today and I am delighted with the victory,” said Degenkolb after the race. “It is really great to win in my home country. The team worked very hard throughout the whole race and gave me a great lead-out.
“We reacted well on the late attacks in the finale. For the sprint I had the right position and could come through at the right moment, so that was fantastic.”
It’s Degenkolb’s second win of the season after he took a stage victory in the Arctic Race of Norway in August, also finishing the race with the points classification jersey.
Degenkolb has been named in Germany’s squad for the 2016 UCI Road World Championships in Doha, Qatar, in mid-October where he will line up for the road race with fellow sprinter Marcel Kittel.
Degenkolb will leave Giant-Alpecin at the end of the 2016 season and will join American WorldTour team Trek-Segafredo.