Among retirements were Bradley Smit, Aleix Espargaro, and Dani Pedrosa, with the latter retiring with a crash after making contact with Zarco in the opening lap.
A delayed start was announced and Miller was given a five row start on the rest of the field, then as the field up after the sighting lap Marc Marquez staled his Honda and push started it and inexplicably rode against the circuit to take his place on the grid, a move that saw him suffer a pit lane ride through penalty dropping him from first to nearly last.
The head of the DORNA group that runs MotoGP, Carmelo Ezpeleta, on Tuesday told Radio Marca that he would talk to Marc Marquez and Valentino Rossi after the Italian accused the Spaniard of deliberately crashing into riders at Sunday's Argentina GP.
Crutchlow bided his time in the race to the closing stages before taking the lead only for Zarco to re-pass him before Cal got back underneath the Frenchman to win the race. However, as a penalty, all the riders were made to start from the back of the grid, while Miller would start from pole.
Marquez was charging through the pack following his penalty when he came up on Rossi.
Suzuki's Rins secured a maiden MotoGP podium result with pole-sitter Miller having to settle for fourth place for Pramac Ducati.
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The tricky weather conditions in Argentina led to chaotic scenes before the race even began, as Jack Miller was the only rider to make the decision to change to slick tyres in time. The previous race victor and Factory Ducati rider Andrea Dovizioso will start from eight, whereas his teammate and two-time world champion Jorge Lorenzo could do no better than 14th spot on the grid.
With six laps to go, Miller had a major moment at Turn 13 and gave up the lead to Crutchlow and dropped back from the lead battle.
"I did not make anything insane with Valentino", he explained. He added: "I'm scared, I'm scared on the track when I am with Marquez".
"But from Friday morning, he make like this with [Maverick] Vinales, [Andrea] Dovizioso, he make like this with me in Saturday morning-and today in the race he go straight to four riders, because he do [es it] purposely".
Rossi finished 19th, with his Honda rival one place ahead of him after he received a penalty.
The LCR Honda rider however, regained the lead on the penultimate lap with Zarco coming in hot and managed to take his career's third win, while denying Zarco his first ever. Andrea Dovizioso finished sixth, just in front of Tito Rabat who wrapped up a solid weekend with a great result in seventh.