Giant-Shimano rider Kittel beat Peter Sagan (Cannondale) in the sprint for the line at the end of the 122km stage from Dubai to Palm Jumeirah, with time trial winner Taylor Phinney (BMC) finishing third to stay in control of the general classification.
Omega Pharma QuickStep's sprint star Cavendish was the story of the day, however, getting himself boxed in over the final few hundred metres and not even getting into contention for the stage win.
“The team did a great job in bringing me into position,” Kittel said.
“We did a lot of work and then in the last 500 meters I had do work for myself and then I started my sprint with 200 meters to.
"I’m very proud of how we worked for the win today. There was a lot of wind and I hope it’s better in the next few days."
Friday's stage three of the four-day race is a 162km ride from Dubai to Hatta.