The German speedster from Argos-Shimano beat Davide Appollonio (Ag2r-La Mondiale) and Nacer Bouhanni (FDJ) to the line at the end of the 162km opening stage from Al Musannah to Sultan Qaboos University.
Bobbie Traksel (Champion System) and Kohei Uchima (Japan) escaped almost immediately and built up a nine minute advantage after the only King of the Mountains climb after 45km at Al Awabi.
But the gap had dropped to 7:20 at the first intermediate sprint after 65km with Kittel's Argos team-mates and GreenEdge leading the bunch. And the advantage had been whittled down to 4:30 inside the final 40km.
They were caught with 16km to go to set up the gallop to the line where the Argos-Shimano sprint train worked perfectly, after struggling at the Tour Down Under and Tour of Qatar, to allow Kittel to take the red jersey of overall leader via the 10 bonus seconds for the stage win.
Alexander Kristoff (Katusha) and OPQS leader Tom Boonen, in his season debut after recovering from injury, completed the top five. Wiggins was forced to check up behind a crash with two kilometres remaining - arriving home one minute and 21 seconds down but with the three kilometre rule expected to be applied. Christian Knees led the team home.
The race has attracted a number of big names including Bradley Wiggins, Chris Froome, Alberto Contador, Cadel Evans, Vincenzo Nibali and Joaqium Rodriguez who are expected to shine on stage four and the ascent of Green Mountain.
But Tour de France champion Wiggins lost 1:21 and is last overall in the general classification after a late crash caused a split in the peloton.
Peter Velits won the third staging of event last year and returns to defend his title in the six-stage event which is rated at 2.1 on the UCI Asia Tour.
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