Boonen and his Omega-Pharms Quick Step were careful to protect his lead on the sixth and last stage, 120 kilometers (75 miles) from Sealine Beach Resort into Doha Corniche.
He finished the stage 15th, happy to track Tyler Farrar, who was sixth, and beat the American by 28 seconds overall to add to his tour victories in 2006, 2008 and 2009.
"It is always nice to win here in Doha. Whether it is the first stage or last, I feel at ease in Qatar," Boonen said.
"We had a good lead going into the final stage and I wanted to ride safe without any mishap.
"I am glad to start the season with a win and now I can look forward to the classics. My team did a great job this week."
Farrar, riding for Garmin-Barracuda, was followed in the overall by Spanish rider Juan Antonio Flecha of Sky Procycling, 33 seconds back, then Boonen's teammate Gert Steegmans, 34 seconds down.
The stage was won by Arnaud Demare, the under-23 road world champion, for his first pro win.
Russia's Denis Galimzyanov of Katsuha was second, and last year's winner, Australian Mark Renshaw of Rabobank was third.
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