Pedrosa lapped the Texan circuit in 2:04.408s, the fastest time of the weekend so far, to beat his compatriot by almost four tenths of a second.
That was six tenths fastest than the fastest time on Friday but still one second slower than Marquez managed in the pre-season test.
Marquez had bounced back from an early crash at Turn 13 to run fastest for much of the session but Pedrosa's late improvement left him no time to reply.
Jorge Lorenzo was a further half a second back in third, moving his works Yamaha above Cal Crutchlow's satellite Tech 3 machine with his last lap of the session.
Lorenzo made the gap to the Hondas much more respectable, having been more than a second behind for much of the session. His final effort hauled him above Crutchlow right at the last minute.
Stefan Bradl was fractionally ahead of Andrea Dovizioso in fifth, while Valentino Rossi had a low-key session on the second factory Yamaha and finished seventh fastest.
Alvaro Bautista, Nicky Hayden and Ben Spies completed the top 10 and claimed the final automatic spots in the pole shootout.
Behind them, Aleix Espargaro was the lead CRT machine, beating the satellite prototype bikes of Crutchlow's Tech 3 team-mate Bradley Smith and Andrea Iannone. The rookie pair will now have to fight through Q1 to join the rest of their 'class' in final qualifying.
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