The Bahrain McLaren rider beat stage one winner Bryan Coquard (B&B Hotels-Vital Concept) and Niccolo Bonifazio (Total Direct Energie) to the line.
"It’s good to win in my first race back and it gives me and the team a lot of confidence before the big races that are ahead such as Milan-Sanremo," said Colbrelli.
"I had a bit of mechanical problem early on in the stage, but the mechanic managed to sort that out and then the hardest part were the conditions. Yesterday the heat was intense, today the wind was the issue and made it a very hard stage."
Coquard won the sprint on the opening day of the race but said after missing out on stage two: "I was a bit too far back coming into the final kilometre and we had to make a big effort to move up with 500 metres remaining.
"Colbrelli went very early but he was very strong. I was on his wheel but that’s where I stayed."
The 174.5km stage saw an early breakaway that established an eight-and-a-half minutes advantage over the peloton.
But the gap began to fall and most were reeled in before the final climb up Cote de Monesties.
Emil Vinjebo (Riwal Readynez) was the last man standing but he was caught with 1km to go and Colbrelli powered to victory in a sprint finish.
Stage three should suit the big GC contenders, including Team Ineos duo Chris Froome and Egan Bernal, as it features four significant climbs, including three first-cat ascents.