Yamaha team-mates and MotoGP title contenders Jorge Lorenzo and Valentino Rossi finished opening practice at Indianapolis in first and fifth respectively.
Lorenzo led much of the 45-minute session, but needed to overcome Honda's Marc Marquez to reclaim the top spot in the closing minutes.
The #99's best lap of 1m 33.654s was just under one-second from the official race record and 0.093s clear of Marquez.
“After the summer break I felt great from the beginning, I had a good feeling with the bike and I could keep a good pace until the end,” Lorenzo said. “I was on top of the classification all the time and that's a good sign but we are still far from last year's times. We'll see how to improve and what the other riders will do throughout the weekend.
“The track conditions are more or less the same as last year. In the first session it's a bit dirty but then it's going to improve, as well as it did last year. We still have to test some settings and improve small details but as I said starting so strong and being in the first position is always a good sign.”
Rossi, who starts the second half of the season with a 13-point lead over Lorenzo, was 0.720s slower than the Spaniard.
“The first practice after you are back from the summer break is always difficult but today the feeling with the bike was not bad,” said the Italian. “The problem here is that we struggle a bit with the rear tyre. Already after few laps the tyre suffers a lot and its performances drop down.
“We decided to use the same tyre for the entire session because we aimed to save tyres for the weekend and therefore I was not able to improve my lap time. We have to work, in order to improve this feeling.
“The surface was dirty, as usual on the first free practice, and I believe the tyres suffered a lot because of this, but I think the conditions will improve during the practice.”
FP2 takes place this afternoon.