The German from Argos-Shimano won the race for the second successive year, denying the Briton a record fourth victory in the oldest race in Flanders.
The Omega Pharma Quick Step star was half a wheel length back in second after leaving his dash to the line too late.
Arman Kamyshev (Astana), Gregory Rast (RadioShack Leopard), Jacobus Venter (MTN - Qhubeka), Kenneth Van Bilsen (Topsport Vlaanderen), Stefano Borchi (Vini Fantini) and Mart Ojavee (Champion System Pro Cycling) attacked inside the opening 10km of the flat 204km course and had a four minute lead on the peloton.
Christopher Juul Jensen (Saxo-Tinkoff), Ireland's Matt Brammeier (Champion System Pro Cycling) and Koen Barbe (Crelan - Euphony) bridged the gap to make a lead group of nine with a 4:30 advantage after 45km.
The peloton split behind and that acceleration saw the escapees caught although Brammeier and Borchi persisted with their attack alongside Sven Vandousselaere (Topsport Vlaanderen).
The race concluded with three laps of a 21.4km finishing circuit around Schoten and the trio were caught 35km from home as the sprinters' teams took control at the front of the peloton.
And it was Kittel's formidable lead-out train, with Roy Curvers and Tom Veelers as his final two support men, that put him in prime position inside the final kilometre.
Cavendish was left isolated by team and lost his unbeaten record in the race, following triumphs in 2007, 2008 and 2011, as the German held on.
Barry Markus, Andrea Guardini, Alexander Kristoff, former winner Tyler Farrar, Kenny Dehaes, Theo Bos, Romain Feillu and Michael Van Staeyen completed the top 10.
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