The Repsol Honda rider was quickest around the Laguna Seca circuit ahead of world championship points leader Jorge Lorenzo on the factory Yamaha.
Third quickest was Pedrosa's team-mate and defending world champion Casey Stoner who was forced off the track briefly on his final lap when he was held up by slower riders.
Stoner is to retire at the end of the season but needs to make up ground on Lorenzo if he is to retain his title, the Australian sitting 19 points behind his Spanish rival.
Lorenzo's team-mate Ben Spies was fourth quickest at his home round of the series just days after he announced he would be leaving the factory Yamaha team next season.
In fifth and sixth place were Monster Yamaha Tech 3 team-mates Andrea Dovizioso and Cal Crutchlow who have both been tipped to take Spies' place next season.
Crutchlow, who escaped injury when he suffered a heavy crash going into turn 10, has also been linked with a move to Ducati.
But after announcing he would be staying with Ducati next season American former world champion Nicky Hayden was seventh quickest.
Eighth was Stefan Bradl on the LCR Honda, with multiple world champion Valentino Rossi ninth on the Ducati.
Rossi crashed near the end of the session which was ended prematurely because the safety air fence was damaged by his bike.
San Carlo Honda Gresini's Alvaro Bautista, who crashed at the same turn as Rossi shortly beforehand, came in 10th and like the Italian was unhurt.