He struggled and qualified seventh.
Its only the second time ever in the premier class the reigning champion has failed to qualify in the top six.
Ducati's Alvaro Bautista of Spain rode his machine to the second fastest time, posting 2:00.742, while Yamaha rider Johann Zarco of France was third fastest.
"I will try to learn from him because he is riding very well".
"I had to take my second bike but I didn't feel flawless on it, so I did a la that was good but not good enough", said Marquez, still not content with this qualifying position.
"Also I did a not do a good lap, and for that reason we are seventh".
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Conditions were dry with blustery winds for the MotoGP riders on Saturday but some showers are forecast for race day on Sunday.
The 24-year-old crashed his Repsol Honda in his first flying lap of the session on Saturday, and was forced to use his spare bike, which just magnified the discomfort he was enduring, trying to manage his twitchy bike fast enough around the corners. But he couldn't do much afterwards during the 15-minute Q2 session. "This morning we made a small mistake with the setup and lost the direction a little bit". Then we went left, but was too late. So I think the [riders on the] first row start for the victory for sure. Anyway, we're not happy with today but not completely disappointed either, as our pace isn't bad.
"We'll try and have a good race. It won't be easy because here, every time you go on track the feeling is different, depending on temperature, if it rains or not, and so on, so we'll see what it's like tomorrow and do our best, like always".
If Dovizioso wins the race, then Marquez needs to finish second to become world champion.
"We know it's hard, but the Championship is open and we'll try everything", Dovizioso said at a press conference ahead of the Malaysia GP, scheduled to take place over the weekend.