The Omega Pharma-Quick Step rider sprinted to victory from Oscar Freire (Katusha) and Mark Renshaw (Rabobank) at the end of the 216.8km race.
"I stayed in the safe zone, out of trouble until the last kilometres," said Boonen. "After a week of hard training I didn’t know what I could expect from this race. But today we decided to try and go for a win.
"We worked really hard for the sprint in the finale. The guys were great, perfect team work. The finish here at Paris-Brussels is not so easy - the team led me perfectly until the last corner.
"[Nikolas] Maes literally killed everybody during the leadout. His job permitted me to pass the train of Rabobank and have a good sprint. I’m satisfied about my performance, this race was missing in my palmares.
"It’s an important classic and it’s nice to have it on my personal list."
Lars Bak (Lotto-Belisol), Craig Lewis (Champion System), Andreas Schillinger (NetApp), Georg Preidler (Team Type 1-Sanofi) and Kevin Thome (Wallonie Bruxelles-Crédit Agricole) attacked early in the race, which started in the French town of Soissons, 100km north-east of Paris.
The escapees built a lead of more than five minutes then Preidler and Bak went out themselves with 48km to go.
However all five were sucked back into the peloton with 21km remaining.
Despite a series of attacks in the final kilometres, the race was together entering the Belgian capital. Rabobank took control of the group from Omega Pharma-Quick Step as they entered the final kilometre but Boonen was able to get up with Freire and Renshaw and leave them trailing.
Spaniard Freire was awarded second in a photo finish after Australian Renshaw was originally given the place.