The Belgian star got the perfect leadout from his Quickstep team and finished two bike lengths clear of Simone Cadamuro of Milram with Enrico Gasparotto (Liquigas-Bianchi) just behind in third.
Boonen earned a ten second bonus for his victory and takes the leader's claret jersey into Friday's stage, another flat one which he will start favourite for.
Rik Reinerink (Skil-Shimano) initiated a breakaway after 54km and was joined by Matthé Pronk (Unibet.com) and Koen Barbe (Chocolade Jacques) at the 79km mark.
Schumacher wins after crash
They built a maximum advantage of 5:45 but Davitamon and Discovery, along with Quick Step, dragged the break back and they were eventually absorbed with 11km remaining setting up the inevitable sprint finale.
Boonen said: "Winning the first stage is good for the team's morale. Now we can ride the rest of the race without any pressure.
"But it can get boring when we always set up the sprint for me so during the next few stages we'll try and get riders in the breakaways.
"My team mates such as Steven De Jongh and Wouter Weylandt also deserve a chance to win a stage."
Watch Friday's Stage Two at 15:00 CET on Eurosport or log on to eurosport.com for live updates.
David Kopps it
Hincapie sitting pretty