The Frenchman was part of an early four-man breakaway and held off his rivals in a sprint for the line to triumph in the 208km stage from Saint-Malo to Nantes.
The Confidis rider just edged America’s William Frischkorn (Garmin Chipotle) into second, with France’s Romain Feillu (Agritubel) third and Italy’s Paolo Longo Borghini (Barloworld) fourth.
Feillu though took the race leader’s yellow jersey.
The flat stage, featuring no classified climbs, was certainly one for the sprint specialists, but the wet and windy conditions were not conducive to fast racing.
The leading quartet, whose advantage over the peloton was at one stage almost 15 minutes, managed to hold off the chasing pack in a nail-biting final few kilometres.
They were handed an advantage when the peloton was delayed by protesters from the General Confederation of Labour – one of the largest trade unions in France — blocking the course around 60 km from the finish.
Tour director Christian Prudhomme was forced to step in to urge to them out of the road.
Feillu said after the race: ‘‘It is magnificent to take the yellow jersey.
“Everything went well. We were away for almost 200km. We worked very well together. In the end, I took more turns (at the front) as I was thinking of yellow.”
Frischkorn, Longo Borghini, Feillu and Dumoulin led the four-man breakaway inside the opening 25km.
The quartet continued to force the pace, stretching their advantage over the peloton to more than 14 minutes with around 135km to go.
However, the chasing pack – led by Caisse d’Epargne, Credit Agricole and Team Columbia – started closing inside the final 130km.
The gap to the long-time leaders dropped below 10 minutes 100km out and closed to within five 25km from the line as the Liquigas riders picked up the pace at the head of the peloton.
But it was Dumoulin who came home just ahead of his compatriot Feillu – who was also passed by Frischkorn – after the lead had changed hands a number of times between the two French riders over the final two kilometres.
Today’s stage four – a 29.5km course around Cholet – is the first individual time trial of the tour.