The Belkin-Pro Cycling team rider was playing cat and mouse with Ramunas Navardauskas of Lithuania and Leigh Howard of Australia after the three broke away from the pack as they entered the Edmonton Garrison. The race ended with three laps around the 5.3-kilometre Canadian Forces Base airstrip.
The trio jockeyed for position through the final lap before Vanmarcke left the saddle and jumped inside the pair before the final curve to win the day in three hours, 12 minutes 11 seconds.
"I knew it was a really tricky last 100 metres," Vanmarcke said of positioning himself for the final attack. "I wanted to be in second position in those last corners and it would have been perfect if I could be sprinting just before the last corner and I did. I went full into the last corner, maximum just not to crash."
Navardauskas, who finished second, said he knew that with just 175 metres from the corner to the finish, he needed to be ahead in the corner.
"I was hoping to sit close on the wheels of Sep and try to outsprint him, but Sep had a good handle on his bike and when he went into the corner I heard his tires slipping … I lost like 10 metres on that corner. He knew how to do it."
Tom Dumoulin of the Netherlands finished 11th, about 11 seconds back of Vanmarcke but retained the yellow jersey as the overall leader. Ruben Zepuntke of Germany is eight seconds back and Navardauskas third 13 seconds behind. Canadian Ryan Anderson finished 14th Friday and remains seventh, 16 seconds off the pace.
"The guys at the front were just too strong today," Anderson said. "I just tried to limit the losses as much as possible. Still (it was) a pretty good day."
Stage 3 began in the community of Wetaskiwin and wound its way west and north through the towns of New Sarepta and Fort Saskatchewan. The 160-kilometre ride ended with a circuit finish on the airstrip of the garrison.
The stage is the most level terrain in this year's tour but prevailing cross winds on the open roads did present a bit of a new challenge for the riders at times.
"We thought it would be tailwinds all day and it seemed to be cross winds all day," said Vanmarcke. "A lot of teams tried to split the peloton and it worked but not totally well, there were still two big groups."
As usual there were a number of small breakaways throughout the day but the only one that lasted any significant time came in the early afternoon when Canadian Ben Perry created a 25-second lap about 75 kilometres into the race. Near the 90-km mark he was joined by fellow Canadian Matteo Dal-Cin. The pair had nearly a full minute on the field at one point. They were joined by two other riders but that group was reeled in by a 40-rider group with about 40 kilometres to go.
"I was looking to just get in the break, get some exposure," Perry said of the experience that saw him on his own when the Giant-Shimano team backed off the pack. "I was hoping someone would follow me but no one did so I spent about 10 kilometres riding by myself."
The four were hauled in went they ran into a strong cross-wind section "where the world tour teams really hurt everyone. That totally destroyed our lead."
Perry had a flat tire after dropping into the pack.
"Kind of at the exact moment when you really needed to be in the right place at the right time," he said. "But being off the back chasing at that moment wasn't ideal."