The sprint king failed to make it four individual stage wins on the spin as compatriot Greg Van Avermaet prevailed for Predictor-Lotto.
Van Avermaet was part of a ten-man breakaway that gained two minutes on the peloton, and beat Marcel Sieberg and Stephane Poulhies in a sprint finish.
The 156km trip from Al Zubarah to Mesaieed along flat, desert-lined roads, also saw Boonen lose the race lead.
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Wilfried Cretskens - another Belgian - takes over the yellow jersey for Quick Step.
Friday sees the Tour move on to Sealine Beach in Doha at the end of a 134km stage 6.
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