The 22-year-old came into the stage lying third overall, but with many waiting for an aggressive ride from Sylvain Chavanel it was Dumoulin who stood out and eventually claimed the race lead. He latched onto a dangerous move inside the final 30 kilometres, distancing both Chanavel and overnight race leader Lars Boom (Belkin).
With the chance of taking the race lead increasing with each kilometre Dumoulin buried himself on the run into the final climb to La Redoute.
“I had to work hard for it today,” said Dumoulin after the finish. “I crashed before La Redoute but I stayed calm and was able to come back after a long chase.
The stage was eventually won by Sky’s David Lopez with Stybar finishing fourth and picking up vital bonus seconds that leave him just eight shy of Dumoulin’s lead.
"Tom's good form is not a big surprise to us," said coach Rudi Kemna after the stage. "He took a big step in progression at the Tour so this is a logical result. After the Tour he had a rest period and took care of himself well before preparing for this race with some quality specific training. He showed how driven he was by training on the course itself prior to the race.
"It was a super situation for Tom all day. When Astana did the forcing he was able to follow and he started riding himself into the jersey. He had to work hard to keep a gap over the group behind him but it was the right decision. We are really glad to have the jersey on board, and we will protect Tom as best as possible tomorrow."
The race concludes on Sunday with a 208 kilometre stage from Tienen to Geraardsbergen.