Yamaha's Maverick Vinales, the 2016 race winner on a Suzuki, starts fourth.
Marquez leads Italian Andrea Dovizioso, who qualified sixth for Ducati, by 16 points in the standings with Rossi fourth and 33 points behind the Spaniard.
Rossi's time was a mere 0.084 slower than Marquez, whose lap of one minute 59.941 seconds was a record by a MotoGP rider at the circuit.
Sunday's race starts at 1430GMT, avoiding a clash with the Belgian Formula One Grand Prix at Spa-Francorchamps which gets under way at 1200GMT.
(Reporting by Alan Baldwin, editing by Clare Fallon)
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