Driving a Ford Fiesta WRC, Rossi defeated former Le Mans driver Dindo Capello's Citroen by 2.8 seconds after nine stages. Rossi had previously won the event in 2006 and '07.
Fellow MotoGP stars Andrea Dovizioso and Jorge Lorenzo finished fifth and 10th.
Rossi also won the Masters Show contest in a final shoot-out with Capello.
Having only secured three podium finishes in two tough MotoGP seasons with Ducati, Rossi is counting on his return to Yamaha to help him recapture the form that brought four titles and 46 race wins in his previous seven-year stint with the team.
His last victory came in 2010's Malaysian Grand Prix, and he hopes the Monza success is a good omen.
"This is more than a normal victory," Rossi told Gazzetta dello Sport.
"When you climb on the top step of the podium it's always special, but most of all I hope this is the turning point after two difficult seasons, unfortunately difficult beyond any prediction.
"Let's hope this is the beginning of a new era.
"We need to return to winning ways in MotoGP too."