The victory at Misano, the eastern Italian circuit nearest to his home, was the first in 15 months for the 35-year-old Yamaha rider and ended Honda's 100 percent record for the season.
Spaniard Marquez, who started on the second row and was chasing a record-equalling 12th victory in 13 races so far this year, lost control of his bike with 19 laps to go with the machine slipping out from beneath him under braking.
The 21-year-old then struggled to get the Honda started again with marshals pushing him along.
Yamaha's first win of the year became a one-two with Spaniard Jorge Lorenzo, winner at Misano for the last three years, second for the fourth race in a row after starting on pole position.
Marquez's team mate Dani Pedrosa was third.
Rossi's last win was at Assen in the Netherlands in June last year and Sunday's was the nine times world champion's 81st in the top category and 107 in all classes. It also took his career points tally to a record 5,012.
Marquez saw his championship lead over Pedrosa cut to 74 points from 89, with Rossi a point behind.
ROSSI MANIA
Cheered on by thousands of fans, Rossi snatched the lead after three laps and stayed out front after an early battle with Lorenzo and Marquez to clinch his first win on Italian soil since 2009.
"We knew that to try to win here we needed a hand," he grinned after crossing the line 1.578 seconds clear of Lorenzo.
"And it was fantastic. To come back with the victory, the first of the season, and to make it in front of all the crowd is something special."
The victory capped a weekend of celebration for Yamaha, who were marking the 50th anniversary of their first world championship with Britain's Phil Read.
Marquez's crash, which left him battling back from 20th and last, was his first big race mistake of a season he has dominated and his first fall since the Italian Grand Prix at Mugello in June last year.
The Spaniard had started fourth and off the front row for the first time this year.
He will now have to wait until the next race in Spain, at the Motorland Aragon circuit on Sept. 28, to equal Australian Mick Doohan's 1997 record of 12 wins in a season in the top category - also with the Repsol Honda team.
(Reporting by Alan Baldwin in London, editing by Sudipto Ganguly)
Share
