The Slovakian added the World Tour event to his already illustrious CV that includes six Grand Tour stage wins and the green jersey at the Tour de France at the tender age of 23.
The Cannondale rider attacked out of an 11-man escape group with 3km remaining of the weather-shortened 183km race.
Slovenian Borut Bozic (Astana) and Greg Van Avermaet (BMC) followed Sagan over the line.
There was disappointment for Tom Boonen whose bid to become the only four-time winner of the race ended with a crash while Fabian Cancellara, who was looking to add the second leg of the Flemish cobblestone quadruple after winning Friday's E3 Harelbeke, also abandoned.
And Mark Cavendish's quest to add the race to a one-day Classic palmarès that only includes the 2009 Milan–San Remo was foiled after he failed to make the decisive break.
Things looked promising for the Omega Pharma-Quick Step duo of Boonen and Cavendish as they, and Sagan, were part of a 25-man lead group that formed almost immediately from the start at the coastal town of Gistel after 45km was taken off the route due to snow in the area around the traditional start in Deinze.
Freezing crosswinds caused consternation in a hectic opening hour that saw an average speed of 53km/h but eventually the lead group was caught by 28 chasers.
The peloton regrouped midway through the race only for Juan Antonio Flecha to attack. He was joined by Assan Bazayev (Astana) and Matthieu Ladagnous (FDJ) and they opened up a two minute advantage over the first three of the nine climbs on the parcours.
Boonen crashed after riding on the kerb on the approach to the pivotal Kemmelberg climb before Heinrich Haussler attacked ahead of the second ascent of the Baneberg, the seventh of the nine 'hellingen'.
Sagan was able to bridge the gap to Haussler, the Slovak able to make splits that the likes of Cavendish and Andre Greipel - who lead the peloton over the line in 11th - cannot and a 13-man lead group formed.
Stijn Vandenbergh (OPQS), Sagan's team-mate Maciej Bodnar, Andrey Amador (Movistar), Yaroslav Popovch (Radiosack) and Jens Debusschere (Lotto) were also in the escape and they worked well to build up a 50 second lead.
Bazayev was dropped from the lead group on the second ascent of the Kemmelberg and Cavendish was left frustrated by a lack of team-mates unable to form a coherent chase.
Debusschere then had a mechanical issue to see the lead group down to 11 and the peloton made a steady impression on the flat 42km run to the line after the Monteberg.
Bodnar was dropped from the front group with 5km to go to leave Sagan isolated without a team-mate and with the bunch within 30 seconds, the Slovak made his move.
After finishing second in this race last year and also runner-up in Milan–San Remo and E3 Harelbeke this term, the Terminator would not be denied as he held a 16 second lead going under the Flamme Rouge.
He even had time to do a wheelie as he crossed the line, 28 seconds clear of Bozic and best home rider Van Avermaet, to extend his lead at the top of the World Tour rankings.
Haussler, Flecha, Ladagnous, Eisel, Vandenbergh, Popovych and Amador completed the top 10 with Greipel leading the main bunch over the line, 14 seconds later.