But Atapuma held off a late challenge from Warren Barguil (Giant-Alpecin) to take his first WorldTour win since the 2013 Tour of Poland.
The 23-man breakaway featured many riders making the most of their climbing legs from the Giro d’Italia, including Ian Boswell and David Lopez for Team Sky, and, of course, Atapuma.
It was Atapuma who went off on his own with 6.5km to go, distancing Berhane and Wellens and enjoying a minute’s advantage over the peloton.
Jarlinson Pantano (IAM Cycling) mad the move that split the peloton with just over 3km to go, with three-time winner Rui Costa (Lampre-Merida) and Geraint Thomas among the select group on his tail.
Miguel Angel Lopez (Astana) then tried his luck as the group swept up the battling Wellens, with Atapuma’s lead cut to 37 seconds.
Tejay van Garderen (BMC) put in an attack, cutting into the advantage of his BMC teammate up the road. After a bit of cat and mouse, van Garderen put in another effort with just over a kilometre to go.
Barguil then moved easily past the small group, with van Garderen and co not immediately attempting to close down the young Frenchman.
Barguil had Atapuma in view but couldn’t catch the breakaway rider as the group of favourites sprinted much of the final 500m to try and force some time gaps.
Ag2r La Mondiale’s Pierre Latour takes over the race lead from Peter Sagan after finishing third on the stage, sitting on the same overall time as Wilco Kelderman (LottoNL-Jumbo). Geraint Thomas sits third at five seconds behind and van Garderen is fifth at 18 seconds.
Stage six sees more mountains and another summit finish in Amden.
Tour de Suisse 2016 stage five, Brig/Glis › Carì (126.4k)
1. Darwin Atapuma (Col) BMC, in 3-41-54
2. Warren Barguil (Fra) Giant-Alpecin, at 3s
3. Pierre-Roger Latour (Fra) Ag2r La Mondiale, at 7s
4. Tejay van Garderen (USA) BMC, at 9s
5. Wilco Kelderman (Ned) LottoNL-Jumbo, st
6. Geraint Thomas (GBr) Team Sky, at 12s
7. Andrew Talansky (USA) Cannondale, st
8. Rui Costa (Por) Lampre-Merida, at 16s
9. Michele Scarponi (Ita) Astana
10. Miguel Angel Lopez (Col) Astana, all same time
Overall standings after stage five
1. Pierre Latour (Fra) Ag2r La Mondiale
2. Wilco Kelderman (Ned) LottoNL-Jumbo, st
3. Geraint Thomas (GBr) Team Sky, at 5s
4. Warren Barguil (Fra) Giant-Alpecin at 16s
5. Tejay van Garderen (USA) BMC, at 18s
6. Andrew Talansky (USA) Cannondale, at 19s
7. Gorka Izaguirre (Esp) Movistar, at 27s
8. Ion Izaguirre (Esp) Movistar, at 30s
9. Miguel Angel Lopez (Col) Astana, at 34s
10. Jarlinson Pantano (Col) IAM Cycling, st