He is now unlikely to be challenged by the man considered his pre-race main rival, Alessandro Petacchi, after the Italian finished the day five minutes in arrears.
Brazilian Murilo Fischer finished third behind Rabobank rider Brown, who on Monday was accused of causing mayhem in the bunch sprint during which Tom Steels crashed and was left with a broken collarbone.
After just a few hundred metres on Wednesday the T-Mobile and Rabobank teams contrived to blow the stage apart. Their tactic worked, but ultimately left Boonen on the podium after 30 leaders left Petacchi and the rest of the bunch in their wake.
Aided by a strong tailwind, the leaders completed nearly 59km in the first hour and went on to build a virtually unassailable lead.
1. Tom Boonen (Quick Step, Bel) 9hr 27min 52secs
2. Steven De Jongh (Quick Step, Ned) at 27secs
3. Bernhard Eisel (T-Mobile, Ger) at 33secs
Boonen was attacked by a few of his more fearful rivals in the closing kilometres, but the Belgian brought them all back to heel on his own before dominating Brown at the finish line.
"I really enjoyed myself today," Boonen said. The Belgian now has 13 victories in four years of racing at the Tour of Qatar.
"The hardest thing was to try and counter the attacks in the final three kilometres. They were going off all over the place, but I never panicked."