The Quick Step Floors rider, who crashed in the opening stage of the four-day race on Wednesday, outsprinted Australian Caleb Ewan after the Orica Scott rider raised his arms in celebration a little too soon.
Briton Mark Cavendish (Dimension Data), who won the first stage after Kittel and Ewan crashed, had to settle for third but retained the overall lead.
Saturday's third stage looks set to decide the race winner as the grand tour specialists tackle the a 10-km (6-mile)climb and hilltop finish at Jebel Hafeet.
(Reporting by Julien Pretot; Editing by Louise Ireland)
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