Their compatriot Dani Pedrosa will start third on the grid for Honda ahead of Britain's Cal Cruchlow of Monster Yamaha.
Seven-times world champion Valentino Rossi, the winner at Indianapolis in 2008, was ninth fastest as the Italian looks for his second victory of the season.
The 20-year-old Marquez enters the 10th race of the campaign with a 16 point advantage over Pedrosa and a 26 point lead over defending world champion Lorenzo.
But there was disappointment for the home crowd on Saturday as Spies, who was returning to action for the first time since his injury in the second race of the year in Texas in April.
Spies was thrown over the front of his bike at turn four in morning practice and his Ignite Pramac Racing team officials said 2009 World Superbike champion had dislocated his shoulder.
Local interest will focus on Ducati's Nicky Hayden, who was sixth fastest in qualifying, and Colin Edwards, who was 12th for NGM Mobile Forward Racing.
(Reporting by Simon Evans, Editing by Ken Ferris)
