Frenchman Guintoli, who sits fourth in the race for the world title, zipped around the Sepang track in a best time of two minutes and 3.002 seconds.
And that was enough for him to edge standings leader Tom Sykes (+0.106secs) and Davide Giugliano (+0.135secs).
In steamy conditions, Guintoli gave himself momentum ahead of Sunday’s two races with an impressive showing.
Guintoli, who last won a race at Assen in April, will be joined by Kawasaki’s Sykes and Giugliano of Ducati on the front row on Sunday.
Toni Elias (Red Devils Roma Aprilia), Marco Melandri (Aprilia) and Loris Baz (Kawasaki) were fourth, fifth and sixth respectively.
Baz was showing excellent speed on one particular lap, but crashed, forcing him back down to sixth.
PATA Honda World Superbike’s Jonathan Rea – who sits second in the standings, 26 points behind Sykes – endured a disappointing session and finished 10th.
Alex Lowes (Voltcom Crescent Suzuki) and David Salom (Kawasaki Racing Team) won spots in the second superpole session, after finishing in the top two of the first, and finished ninth and 12th respectively.
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