The Slovakian responded to a late attack from Stijn Vandenbergh, settling in third behind Geraint Thomas before hitting the front in the closing stages.
Sagan was already upright as he crossed the line, such was his superiority in the showdown, as he finished ahead of Niki Terpstra and Thomas, with Vandenbergh in fourth.
"I want to thank the team today, especially my teammate who has the same size bike as me and swapped bikes with me after about 100km," said Sagan.
"I didn’t think the race would go well but I felt better and better. The finale was tough and there was a lot of crashes. On the Oude Kwaremont when we caught the break, I attacked to create a small group and we managed to go all the way to the finish.
"It's good for me to win, it has helped me bounce back after Milan-San Remo."
Despite being hot favourite for the opening monument of the season in Italy, Sagan finished a disappointing 10th in testing conditions as Norway's Alexander Kristoff earned a surprise win.
1. Peter Sagan (Slovakia / Cannondale) 4:56:30"
2. Niki Terpstra (Netherlands / Omega Pharma - Quick-Step) ST
3. Geraint Thomas (Britain / Team Sky)
4. Stijn Vandenbergh (Belgium / Omega Pharma - Quick-Step)
5. Sep Vanmarcke (Belgium / Belkin) +1:30"
6. Tony Gallopin (France / Lotto)
7. Borut Bozic (Slovenia / Astana) +1:40"
8. Tyler Farrar (U.S. / Garmin)
9. Fabian Cancellara (Switzerland / Trek)
10. Greg Van Avermaet (Belgium / BMC Racing)
- Sports & Recreation
- Stijn Vandenbergh
- Geraint Thomas
- Peter Sagan
- Niki Terpstra