Casey Stoner beat Jorge Lorenzo to the quickest time in Friday practice at a sunny Indianapolis.
Championship leader Lorenzo had dominated much of the hour, taking the lead 15 minutes in and then steadily chipping further fractions off his time.
Stoner was his closest rival but kept falling short - until with 16 minutes to go the Ducati rider produced a 1m40.884s lap to beat Lorenzo by nearly half a second.
Although the Yamaha rider closed that gap down to 0.225 seconds by the end of the session, Stoner remained on top.
Nicky Hayden took third on home ground despite crashing his primary Ducati at Turn 13. He appeared to be nursing his already-injured arm as he walked away, but seemed to have escaped further damage.
Dani Pedrosa (Honda) and Valentino Rossi (Yamaha) improved to fourth and fifth by the end, having earlier languished further down the top 10.
All three of MotoGP's Americans were in the top eight, with Tech 3 Yamaha duo Colin Edwards and Ben Spies sixth and eighth, split by the second works Honda rider Andrea Dovizioso. Spies was another man to fall late in the session.
Aleix Espargaro was an impressive ninth on the Pramac Ducati, followed by the two Gresini Hondas.
Hiroshi Aoyama completed 26 laps for Interwetten Honda on his return after a two-month lay-off with back injuries, and was 16th ahead of LCR Honda's Randy de Puniet, another man still recovering from an injury.