The Omega Pharma-Quick Step rider crossed the finish line in three hours, 56 minutes and 47 seconds with a powerful finale in front of his home town fans.
The Belgian finished ahead of Andre Griepel of Lotto Belisol and Katusha's Alexander Kristoff in a wind-blighted 190km race after being set up for the home straight by his team-mates following the reformation of a two-part peloton.
"I am preparing simply, without stress," Boonen said following the win.
“It’s really a collective victory because my team-mates did a great job to set up a great lead-out train."
“When the day is difficult, I know that I have a good chance in the sprint against the specialists and that was the case again today.”
Boonen admitted the windy conditions made the day tough, but that it played directly into OPQS's hands.
“The weather was ideal for making the race hard,” he said. “Our strategy was effectively to make the race hard from the start, create echelons and that worked perfectly.”
The second and concluding stage sees the cyclists return to Rotterdam from Antwerp on a shorter and more intense route on Saturday, setting up a big final day for the sprinters.