Third on the grid, defending champion Marquez admitted a mistake at a corner had cost him a better time but he will have been buoyed that his closest rivals Andrea Dovizioso and Maverick Vinales will start well back.
Ducati's Dovizioso, who is second in the championship race 16 points behind Marquez, will start ninth on the grid, with third-placed Vinales 14th after he failed to get his works Yamaha into Q2.
"Honestly on the fastest lap, I did a big mistake on the last corner and I lost a lot of time," three-times MotoGP winner Marquez said track-side.
"This time maybe I sacrificed a little bit to attack more.
"But anyway, happy to be on the front row which was the main target. And we are there, we are in front of our main rivals."
Aprilia's Aleix Espargaro will start fourth on the grid ahead of fifth-placed Jorge Lorenzo and Honda's Dani Pedrosa.
Twenty-eight points behind Marquez and with three races remaining after Motegi, Vinales' title hopes have waned in Japan with his Yamaha struggling badly for grip during wet practice sessions at the hinterland circuit in Tochigi prefecture.
He was further frustrated on the drying track in Q1, finishing fourth in the session, with Pol Espargaro and Brad Smith posting the fastest times to graduate to Q2.
His Yamaha team mate Valentino Rossi has also had a forgettable weekend with grip problems and will start 12th in Sunday's race after falling from his bike in the final practice session.
(Reporting by Ian Ransom in Melbourne; Editing by Sudipto Ganguly)
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