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Marquez fought off the leading group of eight riders to clear out and win the race by 1.799 seconds from Yamaha duo Valentino Rossi and Maverick Vinales.
The victory extended Marquez’s lead on the world standings by a further 22 points over Andrea Dovizioso with two races remaining in Malaysia and Spain.
It was the 24-year-old Spaniard’s 35th MotoGP win from 88 starts after he claimed his 44th premier class pole on Saturday.
Italian Ducati racer Dovizioso paid for an early run off and was only able to claw back some lost ground from 20th to 13th to hand the world championship ascendancy firmly to Marquez.
“I went out quietly and tried to warm the tyres and to be calm, but by the second or third lap I got my first contact from Johann Zarco,” Marquez said.
“I could see that this was going to be tough, it was a big group and I started to realise in the middle of the race that I needed to attack or they will overtake me.
“So it was a little bit dangerous at times but with eight or nine laps to go I decided it was time to attack, time to open up a small gap that made my life a little bit easier.”
It was Marquez’s sixth win of the season and he was starting off the pole for the fourth successive year in Australia.
– ‘A great race’ –
It was one of the most aggressive and hard-fought scraps of the season with continual passes as the lead chopped and changed in a nerve-tingling five-way jostle.
It was the second MotoGP win for Marquez at Phillip Island after his victory in 2015, while he has crashed out twice when leading the race.
“With a 33-point lead I am feeling really good with the bike, I even have extra confidence, but now is not the time to do something stupid and plan with my team to organise myself for the last two races,” Marquez said.
Marquez took charge of the race seven laps from the chequered flag and steadily pulled away from the pack, leaving Rossi, Vinales and Zarco to fight for the other podium places.
Vinales dived past Frenchman Zarco in the home straight to snatch third place.
His team-mate Rossi, who has six wins in the premier class at Phillip Island, used all of his guile and experience to take the runner-up spot.
The legendary Italian only resumed racing last month just three weeks after double leg fracture surgery.
“The level of aggression and contact during the race raised a lot, either you get angry but that changes nothing so this is the game if you want to play,” 38-year-old Rossi said.
“It’s a bit more dangerous, but this is way you have to stay on top. I enjoyed it very much. It was a great race.”
Last year’s race winner Cal Crutchlow was fifth with Italian Suzuki racer Andrea Iannone sixth and Australian Honda rider Jack Miller in the points in seventh place after leading for the opening three laps.
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