Fabian Cancellara (Trek Segafredo) finished fourth and Milan-San Remo champion Arnaud Demare (FDJ) won the bunch sprint for fifth place.
It was Sagan's first victory with the world champion's rainbow jersey, after finishing second in five races so far this season.
“I'm very happy that I've won finally with this jersey. It's an important race for me also - it’s the second time I have won here," Sagan said.
"I want to dedicate this victory to my father in law as he had a hard time yesterday and I'm very happy to have won this race for him, and for our team owner, Oleg Tinkov.”
The race lived up to its gruelling reputation, with riders battling strong winds as they tackled 10 climbs over a 243km route, including two ascents of the Kemmelberg.
It was Kuznetsov who animated the last 50km of the race with a solo effort, but Sagan, Vanmarcke and Cancallara bridged after the latter attacked on the Kemmelberg.
The Etixx-QuickStep team of three-time winner Tom Boonen and Niki Terpstra chased hard to close down the all-star break but were foiled as the gap quickly increased.
With 5km of the race left and a 45 second time gap, the race was to be decided with a sprint. At less than 2km to the finish, the breakaway slowed, looking at each other to see who was going to make their move.
Finally after Cancellara feigned an attack, Kuznetsov went and Sagan followed, using the Katusha rider to lead him out and take the win in the sprint.
“The final was very hard because we were in a breakaway. I wasn’t going to make the same mistake as before and pull until the finish," Sagan said.
"We had a gap, I started from third position, and I said I had to go behind him and he pulled me in a very good sprint.
“In the final it was a hard race with the strong wind and we went full gas. In the final we attacked with Fabian in the last cobblestone climb, Kemmelberg, and made the breakaway.
"We worked well together from the start. In the sprint the speed was very slow as we spent a lot of time on the front of the group."
The race was marred by a serious crash involving Antoine Demoitie. He was rushed to hospital in a serious condition after he was struck by a motorbike following a fall.
"Antoine Demoitie is in Lille hospital after a serious crash with a motor bike in Gent-Wevelgem," team Wanty-Gobert confirmed on its Twitter account.
The Tour of Flanders will be held next Sunday followed a week later by Paris-Roubaix. Both races will be broadcast live on SBS/HD and streamed online here at Cycling Central.
Sep Vanmarcke (L), Peter Sagan (C) and Viacheslav Kuznetsov (AAP) Source: AAP
