Atapuma finished four seconds ahead of Warren Barguil and seven in front of Latour on the 126.4km stage from Brig/Glis to Carì.
He was a member of a strong 24-rider breakaway selection which formed 20km of racing. As the breakaway reached the final climb of the day, it was down to a small group of riders to battle it out on the climb.
As the breakaway reached the top of the first long ascent, the Furkapass, the gap to the peloton was two and a half minutes.
The break disintegrated halfway up the climb, with Atapuma the first over the top. With seven riders left in the lead he then attacked solo with six kilometers to go, and managed to hold off the chasing group in the final hundred meters.
"I looked at the stages of the Tour de Suisse and as this one finished at a high altitude and the two climbs before were also high, I knew it would suit me," Atapuma said.
"If the altitude is more than 2000 metres it suits me well. I trained at altitude in the lead up to race to stay focused and motivated."
"I was confident when the breakaway reached the final climb as we still had a reasonable gap. I knew that there were two possible scenarios that were good for the team.
"If Tejay (van Garderen) attacked from behind, then I would be there to help him. Or, in case I got close to the finish as we eventually did, I would attack for the win."
Latour leads the general classification in the same time as Wilco Kelderman (LottoNL-Jumbo), with Geraint Thomas (Sky) is third overall at five seconds.
"My teammates worked hard for me all day long. At 150 meters from the finish line, I attacked," Latour said. "It was so hard but I finished third.
"I didn’t expect to take the jersey in this race. I aimed at a good ranking, a stage victory and to learn for the future in a hard stage race.
"There are two hard mountain stages and a time trial to come and I will fight to keep it. We have a great team, very united."