Van Avermaet of BMC Racing formed part of a nine-man breakaway but moved into a solo lead with 17km to go and pulled away to win by 2min 24sec from runner-up Thomas De Gendt riding for Lotto Soudal and 5min 4sec from third-placed Rafal Majka of Tinkoff.
A heavily thinned-down peloton containing Team Sky’s Chris Froome and Nairo Quintana of Movistar crossed the line in Le Lioran three seconds after Majka, but Contador of Tinkoff was distanced on the day’s final climb and finished 33 seconds later.
Van Avermaet began the day 18 seconds off the yellow jersey but now moves to the top of the general classification and opens up leads of 5min 11sec over second-placed Julian Alaphilippe of Etixx – Quick-Step and 5min 13sec over third-placed Movistar rider Alejandro Valverde . Froome and Quintana are 5min 17sec down in fifth and seventh respectively, but Contador is now 6min 38sec back, 1min 21sec adrift of his two main rivals for overall victory.
Previous race leader Peter Sagan of Tinkoff was left behind when the pace in the peloton soared over four back-to-back climbs in the final 50km, while 2014 Tour and 2016 Giro d’Italia winner Vincenzo Nibali riding for Astana was also dropped early as his general classification hopes collapsed. Van Avermaet, who won a stage of last year’s Tour, said: “It’s a special moment, one of the nicest of my career.”
Stage five took the riders 216km from Limoges to Le Lioran ski station and did not look like a day for a breakaway winner given gaps in the general classification were still tight.However, when Van Avermaet, De Gendt and Andriy Grivko of Astana attacked out of the initial nine-man escape, they were bizarrely allowed to open up a lead of more than 15 minutes as Sagan’s Tinkoff and rival teams Movistar and Team Sky engaged in a stand-off.
Team Sky finally upped the ante ahead of the final barrage of climbs, but then Movistar took over and set a blistering pace that blew the peloton to pieces and led to the likes of Sagan, Nibali and Sky duo Mikel Landa and Wout Poels being dropped. The Spanish team only slowed when the gap was down to six minutes, by which point Van Avermaet had attacked and was leading on his own. It then looked like the favourites would finish together, but a small attack from Romain Bardet riding for Ag2r-La Mondiale at the summit of the final climb prompted a rise in speed that Contador couldn’t deal with, while Team Sky’s Geraint Thomas also lost 16 seconds.
The Tour continues tomorrow with a 190.5km stage from Arpajon-sur-Cere to Montauban.
Stage five result
1 Greg Van Avermaet (Bel) BMC Racing, 5:31:36
2 Thomas De Gendt (Bel) Lotto Soudal, +2:24
3 Rafal Majka (Pol) Tinkoff, +5:04
4 Joaquim Rodriguez (Esp) Katusha, same time
5 Dan Martin (Irl) Etixx – Quick-Step, +5:07
6 Bartosz Huzarski (Pol) Bora-Argon 18, st
7 Julian Alaphilippe (Fra) Etixx – Quick-Step, st
8 Adam Yates (GB) Orica-BikeExchange, st
9 Chris Froome (GB) Team Sky, st
10 Tejay van Garderen (USA) BMC Racing, st
15 Nairo Quintana (Col) Movistar, st
22 Alejandro Valverde (Esp) Movistar, st
23 Geraint Thomas (GB) Team Sky, +5:23
30 Alberto Contador (Esp) Tinkoff, +5:40
1 Greg Van Avermaet (Bel) BMC Racing, 25:34:46
2 Julian Alaphilippe (fra) Etixx – Quick-Step, +5:11
3 Alejandro Valverde (Esp) Movistar, +5:13
4 Joaquim Rodriguez (Esp) Katusha, +5:14
5 Chris Froome (GB) Team Sky, +5:17
6 Warren Barguil (Fra) Giant-Alpecin, same time
7 Nairo Quintana (Col) Movistar, st
8 Fabio Aru (Ita) Astana, st
9 Pierre Rolland (Fra) Cannondale-Drapac, st
10 Dan Martin (Irl) Etixx – Quick-Step, st
22 Geraint Thomas (GB) Team Sky, +5:57
25 Alberto Contador (Esp) Tinkoff, +6:38