Germany’s Kittel endured some of the toughest parcours around to edge out breakaway rivals Juan Jose Lobato (Movistar) and Peter Sagan (Cannondale), with Britain's Mark Cavendish once again failing to feature in the sprint to the line.
The peloton split by some margin on the final climb of the day, seven kilometres from the finish.
Several breakaway attempts were shut down before Kittel made the successful move near the end, having kept a relatively-low profile throughout the arduous stage.
“It was really hard, for me I had exactly enough power to pass those climbs,” said Kittel.
“If they had been one-kilometre longer I would have been dropped. I knew the final before the stage, I knew I had a 50/50 chance. I’m happy to make it.
“In general the team helped me as much as possible, they kept me out of the wind so I could save enough for the last climbs. On the last climb it was every man for themselves.
“Our strategy was to see who was left after the climbs; although it was a bit more difficult without the lead-out, I’m glad I could still make it.”
Race leader Taylor Phinney (BMC) looks set to seal overall victory after remaining top of the General Classification with help from British team-mate Steve Cummings.
Saturday’s fourth and final stage finishes in the shadows of the Burj Khalifa and also looks likely to finish in a sprint, working to American rider Phinney’s advantage.
“We had virtually no help from any other teams today,” Phinney said.
“They [his BMC team-mates] did an amazing job today. I felt good on the climbs, I tried to keep things together, stay up there, and have a bit of fun.
“I was super motivated to keep this jersey, and I’m pleased to pass this test.”