Italian Andrea Iannone qualified third for Ducati despite a fall towards the end of the session.
Rossi, winner of the previous race in Spain, will start seventh and was outqualified by both the non-works Tech3 Yamahas.
Marquez leads Lorenzo by 17 points overall with Rossi a further seven points behind after four races.
(Reporting by Alan Baldwin, editing by Toby Davis)
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