Greg van Avermaet finished second 28 seconds behind after outsprinting Gilbert’s teammate Niki Terpstra and Dylan van Baarle from Cannondale-Drapac.
“To win the Tour of Flanders is something very special. Because I was wearing the Belgian champion jersey people recognised me and I had a lot of support,” said Gilbert, who has also won the Liège–Bastogne–Liège and Giro di Lombardia during his career.
“It’s a monstrous ride by Philippe Gilbert which I think it will go down as one of the most historic rides in the Tour of Flanders.
I cannot remember a ride like this in all my year of commentating,” said Eurosport’s Sean Kelly, who finished runner-up in the Ronde on three occasions during his career.
Gilbert made his move on the Kwaremont with 55km to go from a breakaway group of 21 riders, which had formed after the day’s main break of eight riders were caught by a group of 13.
The group of 13, which did not include defending champion Peter Sagan or Van Avermaet, formed when 2012 champion Tom Boonen attacked on the Muur van Geraardsbergen in his final appearance before he suffered mechanical trouble. This ultimately led to him having to change bikes three times.
In the chase group Sagan made his expected move on the Oude-Kwaremont with 17km to go but fell after clipping his handlebars on the side railings, bringing down pre-race favourite Van Avermaet and Oliver Naesen with him.
Van Avermaet was able to remount but Sagan required a bike change which effectively ended his chances of winning.
A tiring Gilbert crested the final climb, Paterberg, with an advantage of just under a minute leaving him to defend his lead over the final 13km into a strong headwind.
He was chased by Dylan van Baarle, Van Avermaet and Terpstra with van Baarle and Van Avermaet doing the lion’s share of the work.
More results from the one day classic can be seen here.