The young Belgian, second in Gent-Wevelgem last season, showed his preference for the Classic contests after a three-man breakaway settled the first such race of the season.
Juan Antonio Flecha secured his third podium finish in six years as he came home third, unable to up his pace towards the end against two better sprinters.
After an early break was pulled back a group of seven experienced Classics riders established a lead that would never be pulled back, the group splintering over the final 20kms as Sky's Mat Hayman and former world champion Thor Hushovd dropped off the pace.
Flecha tried to boot clear of his two Belgian rivals 3kms from the line but despite his urgings all three remained together as they moved towards the finish.
And it was Vanmarcke who surprised Boonen, surging past the veteran on the outside and winning by a couple of bike lengths.
Flecha said: "Vanmarcke was riding well. He was one of the guys you could see was riding strong last year in the Classics.
"Boonen started a bit too early in the sprint but these things happen when you are at the front. No one can guarantee anything until you have crossed the finish line. I ended up in third place I and I can't be disappointed with that."