Boonen was launched to victory by team-mate Steve de Jongh, who also led Quick Step to victory in the race's opening team time trial to claim the race's first gold jersey.
The Dutchman launched the sprint finale about 500m from the line propelling Boonen to the front as Milram's Petacchi gave chase.
The 26-year-old Boonen, who won five of six stages on offer at last year's race, now takes control of the gold leader's jersey.
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Australian Graeme Brown (Rabobank) had his third-place finish annulled after Belgian Tom Steels (Predictor-Lotto) got caught in his wheel and crashed hard into the road just moments before the finish line.
Frenchman Jean-Patrick Nazon (AG2R) took third after Brown was disqualified for the dangerous move and the Netherlands' Kenny Van Hummel (Skil-Shimano) took fourth.
Steels will miss the rest of the race with a fractured left clavicle and is set to return to Belgium on Tuesday or Wednesday for surgery.
De Jongh, meanwhile, finished outside the top-ten in the 135.5-km stage from Al Wakra to Qatar Olympic Committee, but still managed to claim the points at the day's first intermediate sprint.
A five-man break-away made up of Bert Roesems (Predictor-Lotto), Dmitriy Muravyev (Astana), Piet Rooijakkers (Skil-Shimano), Kenny de Haes(Chocolade Jacques), Christophe Riblon (AG2R) went free of the peloton shortly after the first bonus sprint.
De Haes claimed the second intermediate sprint in front of Roesems and Muravyev, but the peloton easily closed the gap toward the end of the stage with Quick Step and the Spanish Saunier Duval team doing much of the early work up front.
With 11 kilometres left to ride and the five leaders within sight, Petacchi's Milram squad moved to the front of the peloton to fend off counter-attack attempts by Saunier Duval and T-Mobile.
When the leaders were caught 5-km from the finish line Roesems attempted a short-lived solo-break, but the combined force of the chasing sprint-teams easily engulfed the 34-year-old Belgian with just over 4-km to go.
Heading into the final sprint Quick Step, Milram and Rabobank battled for position at the front of the peloton, with a Milram train seeming to take the advantage.
Matteo Tosatto shepherded Boonen and de Jongh toward the line, however, with Fabio Sacchi playing the early front-man for his Italian compatriot Petacchi.
After the Milram train took control Boonen stayed right on Petacchi's wheel before De Jongh launched the sprint for the 2005 world champion, who easily claimed the win from Petacchi.
Tuesday's third stage travels 140-km from Dohat Salwa to the Khalifa Stadium in Doha.
Follow LIVE coverage of the Tour of Qatar all this week on Eurosport 2 television!
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