Creskens bagged the golden jersey by 2:09 from Boonen with another Quick Step rider Steven de Jongh in third, a further 35 seconds back.
Friday's stage saw a breakaway after 15km with Kenny De Haes of Belgium, Dane Glenn Bak and Frenchman Emilien-Benoit Berges gaining 7:30 on the peloton only to be absorbed inside the final 10km.
And in the inevitable sprint, Boonen once beat Italian Alessandro Petacchi and Australian Graeme Brown to the line.
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Cretskens said: "I was in the fifth year of the Tour of Qatar. I am very happy to have won this time around. My role was always to support the team. I cannot believe it that I am the champion."
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