Born in San Bonifacio, province of Verona, Rebellin turned professional in 1992 and came to the attention of the cycling world with a string of strong performances during his early years. He suffers from asthma, a disease that will affect his whole career. In 1996 he gained further notice when he thrived in the 1996 Giro d'Italia. Riding for Polti, the young Italian took stage seven and with it led in the general classification, giving him the pink jersey. He held the lead for six stages and finished the Grand Tour sixth overall. Years later he said of the race, "I have won Classics, but the first important win was in the 1996 Giro, winning the maglia rosa with the stage."
Rebellin time trials in 2006
In 1997 he scored his first UCI Road World Cup victories by winning the Clásica de San Sebastián and the Züri-Metzgete (then known as Grand Prix de Suisse). Over the following years he won many Italian classic races, such as the Giro del Veneto and Tre Valli Varesine. In 2001, he won the Tirreno–Adriatico stage race.
During the 2004 season he amassed seven victories, including what was at the time an unprecedented treble win in the Ardennes classics, with wins in the Amstel Gold Race, La Flèche Wallonne and Liège–Bastogne–Liège. Only one rider, Philippe Gilbert, has repeated this feat since, in 2011. Rebellin also scored a number of podium places in top races such as Paris–Nice and the Clásica de San Sebastián. Despite these achievements, Rebellin did not win the 2004 UCI Road World Cup, which went to Paolo Bettini.
In 2005, Rebellin fell short of his triumphs of 2004, but posted yet another solid year. Although he generally concentrated on classics and small tours, he was part of the Gerolsteiner team in the 2005 Tour de France. With a number of solid performances throughout the season but without any individual victories, Rebellin finished as the third-highest ranked rider in the UCI ProTour rankings. Apart from the ProTour races, he only won one race in the 2005 season, taking the first stage of the Brixia Tour.
Rebellin began the 2007 season leading Paris–Nice until Alberto Contador moved him to second in the final stage to Nice. He later finished second in Amstel Gold Race and won the Flèche Wallonne, which made him the oldest ever winner of an UCI ProTour race. He finished second in the UCI ProTour behind Cadel Evans.
Rebellin triumphed early in 2008 with an overall victory in the Paris–Nice. He won the stage race by 3 seconds, ahead of Rinaldo Nocentini. He went on to win the Tour du Haut Var and show strongly in the Ardennes classics with a second place in the Liège–Bastogne–Liège.
Rebellin won the silver medal in the Men's road race at the 2008 Summer Olympics in Beijing. He was a member of a six-man breakaway group and claimed second place in the sprint finish. This medal has now been revoked in light of his doping sentence by the International Olympic Committee.
On 28 April 2015, at 43 years old, Rebellin won the queen stage of the Tour of Turkey, a mountaintop finish concluding in Elmali. He beat riders twenty years younger than him to accomplish this feat. With that performance, he grabbed the leader's jersey, but lost it to Kristijan Durasek on Stage 6. He had to abandon on the last stage since he crashed after hitting a dog.
In 2017, Rebellin rode for the Kuwait–Cartucho.es team, winning three races. After one season with the team, he moved to Sovac–Natura4Ever for the 2018 season.