The reigning world champion led much of the race, pulling out a margin of over four seconds at one point, but Rossi’s decision to use a harder rear tyre paid dividends as he ran Marquez down in the closing laps.
The second clash between them picked up the front wheel of the Honda, dumping Marquez tumbling onto the tarmac. Though he sprinted to his crashed bike, it was too damaged to resume the race.
Race officials investigated the incident and ruled that no action needed to be taken.
“I overtook him in braking, but he is a rider who is all or nothing,” Rossi said.
“He touched me in the corner, then he touched me again as I was accelerating, I think he made a mistake and he crashed.
“It’s a shame because it could have been a great fight on the last lap.”
Marquez was guarded in his thoughts on the incident, coyly telling reporters that “I’ve always said that (Rossi is) my idol and my reference, so you always learn things from him.
“It’s a shame what happened, because we were having a good race!”
Rounding out the podium were Ducati’s Andrea Dovizioso and LCR Honda’s Cal Crutchlow, who passed Andrea Iannone at the final corner to take third place.
Australia’s Jack Miller posted the best finish of his short MotoGP career, taking the chequered flag as the first Open Class machine home in 12th place after a race-long duel with a group of other bikes.
The softer rubber allowed Marquez to run away from the field in the early going, passing a fast-starting Aleix Espargaro’s Suzuki to take the lead halfway around the opening lap.
His lead peaked at 4.3 seconds on Lap 10 - when Rossi’s pursuit began.
The Italian had made a stellar start from the third row to be challenging for third into the first corner, but a bump from Iannone saw him run wide and fall back down to eight.
Steadily he clawed his way forward until he slipped past Dovizioso for second place on Lap 11 and set off in pursuit of Marquez.
“I knew the race was long, so I knew he could have some difficulty,” Rossi said.
“Catching him lap by lap, I could see him far away but coming closer and closer, it was a great taste!”
Marquez was riding on the ragged edge to try and maintain his lead, wildly sliding the rear of the bike into the corners as his rear Bridgestone began to fade.
But what started out as little chips became big chunks as Rossi began pulling whole seconds out of Marquez’s leading margin.
Rossi got better drive onto the long back straight on the 24th lap, pulling alongside the Honda before outbraking it into the Turn 5 hairpin.
Marquez tried to sneak back up the inside on the exit but ran into the blue Yamaha’s fairing, before clanging into the rear of Rossi’s machine as they accelerated towards Turn 6.
The contact pitched the front wheel of Marquez’s bike up into the air, bucking violently upon landing before spitting the world champion onto the tarmac and out of the race.
From there, Rossi ran home to an untroubled victory, further delighting an already loudly-cheering crowd by donning a Diego Maradona jersey on the podium.
Finishing a distant fifth was his Yamaha teammate Jorge Lorenzo, who tried to take the fight to Marquez in the early laps but otherwise looked a shadow of his usual self.
“Honestly, I am very disappointed,” he said.
“I didn’t expect to finish in fifth position. I expected to fight at least for the podium.
“I was was not able to ride as good as Valentino with the hard rear tyre, maybe we needed a softer one to feel better. I didn‘t feel good and I wasn‘t able to ride as I wanted.
“Valentino‘s race was unbelievable, he was able to go faster than anyone else with the harder tyre, he is in an unbelievable shape.”
After three rounds, Rossi leads the championship by six points over Dovizioso with Iannone a further 20 points behind in third. Marquez sits in fifth, 30 points off the championship lead.
The next race is at Jerez in Spain in two weeks’ time.
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