Pinot caught and passed the sole remaining breakaway rider Stefan Denifl with just under two kilometres left to the summit, ending the Austrian rider's hopes of a stage win after spending over 200km out the front.
The win is the second of Pinot's season, having also soloed away to win stage five of the Tour de Romandie in May, and moves him into the leaders jersey in Switzerland.
Denifl was part of an eight-man breakaway, consisting also of his teammate Mattias Brändle and serial escapee Thomas de Gendt.
As the group reached the final climb the group disintegrated, leaving Denifl alone in the final kilometres, holding a four-minute advantage over the small chasing pack with four kilometres to go.
A game of cat and mouse was occurring behind the Austrian rider with Simon Spilak and Thibaut Pinot launching a series of attacks. Denifl's advantage was overcome by Pinot as the climb reached its final 1,500m and the Frenchman sped towards the summit.
Trailing behind was a select group containing Team Sky's Geraint Thomas, who's gutsy ride moves him up to second in the overall standings as yellow jersey holder Tom Dumoulin sacrificed over 90 seconds to fall to seventh.
A month on from suffering serious facial injuries in a crash at the Giro d'Italia, Ag2r-La Mondiale rider Domenico Pozzovivo rode to second place on the stage and into the top-10.
Tour de Suisse 2015 stage five: Unterterzen/Flumserberg- Sölden/Rettenbachgletscher (237.3km)
1. Thibaut Pinot (Fra) FDJ, 6-22-47
2. Domenico Pozzovivo (Ita) Ag2r-La Mondiale, at 34 seconds
3. Simon Spilak (Slo) Katusha, at 37 seconds
4. Miguel Angel Lopez (Esp) Astana, at 43 seconds
5. Geraint Thomas (GBr) Team Sky, st
6. Jakob Fuglsang (Den) Astana, at 1-15
7. Jan Hirt (Cze) CCC Sprandi, at 1-18
8. Sergio Henao (Col) Team Sky, at 1-29
9. Stefan Denifl (Aus) IAM Cycling, at 1-31
10. Tom Dumoulin (Ned) Giant-Alpecin, at 1-37
Overall classification after stage five
1. Thibaut Pinot (Fra) FDJ, 17-42-07
2. Geraint Thomas (GBr) Team Sky, at 47s
3. Simon Spilak (Slo) Katusha, at 50 seconds
4. Domenico Pozzovivo (Ita) Ag2r-La Mondiale, at 55 seconds
5. Miguel Angel Lopez (Esp) Astana, at 1-07
6. Jakob Fuglsang (Den) Astana, at 1-27
7. Tom Dumoulin (Ned) Giant-Alpecin, at 1-32
8. Steve Morabito (Swi) FDJ, at 2-29
9. Sebastian Reichenback (Swi) IAM Cycling, at 2-43
10. Sergio Henao (Col) Team Sky, at 2-46
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