Australians Mick Doohan and Casey Stoner had held the previous record of 12 pole positions in a season.
Yamaha rider Jorge Lorenzo completed the front row, while Stefan Bradl and Ducati rider Andrea Dovizioso qualified on the second row.
Pol Espargaro of Yamaha broke his foot in a heavy crash during practice but will be assessed on Sunday morning to see whether he could race.
Hiroshi Aoyama fell early in the second session of qualifying but will line up 11th on the grid.
Andrea Iannone was ruled out of Sunday's race due to left arm injuries after crashing on Friday.
(Writing by Ian Ransom; Editing by Sudipto Ganguly)
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