Italian great Valentino Rossi led a Yamaha one-two to claim his maiden win of the season at the San Marino Moto GP and launch his bid for a 10th world title.
Rossi, a nine-time world champion in all categories, finished the 28-lap race on Sunday ahead of Spanish teammate Jorge Lorenzo with Dani Pedrosa, on a Honda, in third.
Championship leader Marquez finished 16th after crashing his Honda on the early laps and trailing at the back of the field for most of the contest.
Lorenzo on Saturday had earned the 30th pole position of his career, but first of the season, to top the grid just ahead of Andrea Iannone on a Ducati and Rossi.
But the Spaniard's bid for a fourth successive win in San Marino was kept in check by a rampant Rossi.
The Italian eclipsed his mercurial form so far this season with a composed and determined performance which he admitted was helped by Marquez's misfortune.
"I'm very happy. It was a great race," an ecstatic Rossi told Sky Sports.
"Obviously incidents like the one affecting Marquez don't happen very often.
"But today we knew we had a great chance to win this race.
"I really enjoyed the race, so many people, so many fans. It was a perfect day."
It was Rossi's 81st win in the sport's elite class, allowing the 35-year-old Italian to become the first rider to reach 5000 career points.
Lorenzo, Rossi, and Marquez - who had a great start from fourth - exploded off the grid and opened up a small gap as early as the first lap, with Iannone, Andrea Dovizioso and Pedrosa leading the chasing pack.
Rossi, however, soon had the thousands of local fans in the stands on their feet with a deft overtaking move on Lorenzo.
By lap six Lorenzo's gap to Rossi began to grow and three laps later the Italian was given a further boost when Marquez lost control on a bend and had to be given help by officials to get going again.
As Rossi pushed on solo, Marquez slipped down the field and virtually out of contention.
The Italian was left virtually unchallenged for most of the remainder but had to fend off Lorenzo in the closing stages before crossing the line 1.57secs ahead of the Spaniard, with Pedrosa completing the podium at 4.2.
With five championship races remaining Marquez remains leader on 289 points but has seen Pedrosa (215) and Rossi (214) close the gap to 74 and 75 points respectively.
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