The BORA-hansgrohe rider finished off his sprint as second-placed Elia Viviani (Quick-Step Floors) banged on his handlebars in frustration. Arnaud Démare (Groupama-FDJ) was third.
"Sprints are always like a lottery and I was wondering what was going to happen," Sagan said. "In the end, I started my sprint early and it worked out. I had the legs to keep going.
"I felt good the second time we climbed the Kemmelberg. It wasn’t too stressful and there wasn’t a lot of wind to make things difficult, which is why we came to the finish in a bigger group.
"It was a different race today from all of the Gent-Wevelgems I’ve ridden and the lack of stress and the better weather conditions made it easier. It wasn’t anywhere near as crazy as the race has been over the last few years, but it was still really fast."
As Sagan celebrated, second-placed Viviani, sat down on the ground and cried with the emotion of missing out on winning a major classic.
"We were confident we could win, the guys were fantastic, and having missed this opportunity makes me extremely sad," Viviani said.
"Gent-Wevelgem is one of my career goals, a race I’ve always dreamt of winning, so it was only natural to have that reaction after crossing the line in second. This is the most disappointing loss of my career and I cried at the finish because I knew I could have won.
"I really wanted the victory and I know it’s a missed opportunity and I’m incredibly sad, but that’s cycling. All I can do is continue working and believing."
Sagan joined a unique club of greats in winning a third Gent-Wevelgem, including Eddy Merckx, Tom Boonen, Mario Cipollini, Rik Van Looy and Robert Van Eenaeme.
