Domenico Pozzovivo (Bahrain-Merida) finished second overall behind Pinot, with Miguel Angel Lopez (Astana) third, both at 15 seconds.
"It's a very important race. Without a doubt, the Tour of the Alps is a mythical race for climbers, so for me to add it to my palmarès is amazing and on top of that to do it against riders of the highest level," Pinot said.
"For me, it's one of the greatest victories of my career. This was the perfect week. We had perfect weather and a perfect route and everything just went even better than I could imagine.
The 21-year-old Padun recorded his first professional victory after he made a late solo break to cross the line alone five seconds ahead of New Zealander George Bennett (LottoNL-Jumbo) with Jan Hirt third at six seconds.
“I can’t believe it,” Padun said. “I’m very happy with my first success as a pro. I’m thankful to my teammates. It was really impressive and everything was perfect today.
"After one hour of racing, I understood that I was feeling well. I knew that I could do something good, but I can’t imagine to take a win. I was thinking how I could manage to go for it. I was dreaming about it and then my dream came true.”
Chris Froome (Sky) finished fourth overall as the Sky leader fine tunes his form for the Giro d'Italia.
“I think I’m a lot closer to being ready for the Giro than I was at Tirreno-Adriatico and we’ve still got two weeks now. It’s been a perfect build-up to the Giro d’Italia," Froome said.
“The team has been fantastic this week and if you look at how they have controlled the race today it’s really impressive. The break had over 10 minutes at one point and in 40km we brought it to under a minute.
“It’s really going to give us an indication of who’s in good shape ahead of the Giro and the team will be selected in the next week or so.”
The race concluded after a 164km run from Rattenberg to Innsbruck, featuring a series of climbs, one of which peaked 12km from home before a 6km descent and a further 6km dash for victory.

Mark Padun. Source: Getty