The second stage which started and finished in Fribourg saw a break of four riders after ten kilometres.
They were caught and another five took over but Cavendish's HTC Colombia team did a lot of work to try and being them back.
With a kilometre to go, riders were all over the shop and it was Bernard Eisel who was followed by Cavendish and Team Sky's Ben Swift.
Cavendish timed his sprint to the line to perfection, leaving Hondo and leader Peter Sagan in his wake.
"It was too hard for a sprint yesterday, but I knew I could get to the finish and win this one. Incredible work by the guys, I probably did the littlest but it was nice to get the win," Cavendish said to Eurosport.
Cavendish had made a gesture as he crossed the line and he said: "My celebration was for all the journalists who know jack sh*t about cycling and they should think about what they say before they say it." after some recent media criticism.
Speaking to his team's press office, Cavendish said: "I've ridden this finishing circuit before and I knew I was in good enough shape for the win. My teammates were amazingly strong. They did some massive turns on the front, and even though the headwind made it hard, they went all out. With all the problems I've had earlier this season they could have lost some faith in me, but they gave it everything."
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