Marquez and Dovizioso are now tied on 199 points with Spaniard Maverick Vinales, who finished fourth for Yamaha, third on 183.
Dovizioso leads Marquez by nine points in the standings with six rounds remaining.
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Jorge Lorenzo was an early race leader, looking nearly untouchable on the factory Ducati until a mistake jettisoned him from the race and allowing hard charging satellite compatriot Petrucci to take the lead - a position he held until Marquez's last lap pass. The former world champion however had an early crash at Turn 6 on Lap 7 which pushed out of the lead.
"I did a good first lap, then I wanted to try the other tyres", explained the reigning world champion who lost his overall lead to Dovizioso last time out in Silverstone.
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The wet is certainly not the ideal terrain for the Yamaha rider who had to settle for fourth place ahead of Pirro and Miller.
Just two-tenths split the top three, whilst fourth to tenth was covered by a further seven-tenths in a closely fought session. The Honda rider made the switch to his second bike with about 17 laps to go, opting for slicks in the hope of the track drying out. Meanwile, Dovizioso couldn't match up to the race leaders but defending his position in third. The final sector had Marquez dive down the inside of Turn 1 and passed Petrucci as he tried a switch-back but failed. Marquez then pulled into the lead and took the win. Seventh over the line was a strong comeback from Scott Redding (Octo Pramac Racing), ahead of a quality ride from rookie Alex Rins (Team Suzuki Ecstar).
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Jonas Folger of Yamaha and KTM rider Bradley Smith finished ninth and 10th respectively, each nearly a minute after Marquez. Fifth in the championship standings is Dani Pedrosa, who endured a tough race, finishing fourteenth. Johann Zarco (Monster Yamaha Tech 3) supplied some late drama as he had a problem on the final lap, but managed to push the bike over the line for the final point.