The European champion, of Team Bahrain Victorious, pipped Belgian Florian Vermeersch (Lotto Soudal) and Dutchman Mathieu van der Poel (Alpecin-Fenix), who were second and third respectively.
Van der Poel, one of the pre-race favourites, came up just short after doing most of the work in a small group chasing Italian Gianni Moscon, who seemed to be heading to victory before a puncture and late crash ruined his chances.
Moscon (Ineos-Grenadiers) eventually finished fourth, 44 seconds off the pace, leaving his compatriot Colbrelli to become the first Italian to win here since Andrea Taffi in 1999.
“Today is a legendary Roubaix with the rain and the weather at the start and an attack with 90km to go after Arenberg,” said Colbrelli.
“I followed only Van der Poel in the finale and in the end I had a super sprint. I was at the limit in the finale. It was super difficult because I had to pay attention for the crashes from the first sectors and then there’s always the stress to be in position on the cobbles. This year is my year, I’m very happy.”
Van der Poel, who was also making his debut on the Paris-Roubaix in the first edition since April 2019 after the Covid-19 pandemic prompted organizers to put off the event, matched his father Adrie’s podium finish from 1986.
Countless crashes marred the race with triple world champion Peter Sagan hitting the deck and Swiss Stefan Kueng going down three times.
Colbrelli spent most of the day tucked into Van der Poel’s slipstream, and when the final sprint on the Velodrome loomed, the Italian was the freshest man.
It long seemed, however, that Moscon would be celebrating a solo win.
Moscon pulled away from a leading group in the cobbled sector of Auchy-lez-Orchies to Bersee 49km from the line as the sun pierced through the clouds and the roads started to dry.
Entering the key cobbled sector of Mons-en-Pevele, Moscon led Vermeersch and fellow Belgian Tom Van Asbroeck by 35 seconds and Van der Poel, Canada’s Guillaume Boivin and Colbrelli by 1:10.
Powering his way through the thick mud, Moscon extended his advantage over the Van der Poel trio to 1:25 as Belgian Wout van Aert faded away.
With 38km remaining, Vermeersch and Van Asbroeck were reined in by Van der Poel and company and the newly formed group organized the chase behind Moscon.
The Italian lost some 30 seconds with a flat rear tire that prompted a bike change 29km from the line with the chasing quintet reducing the gap to 45 seconds.
It fell to 15 seconds after he crashed on a muddy patch, but the Italian stayed just clear as Boivin crashed in the group of chasers in the cobbled sector of Camphin en Pevele.
He was, however, caught and dropped 16km from the finish in the Carrefour de l’Arbre as Colbrelli, Van der Poel and Vermeersch went clear to contest the final sprint.