The morning pacesetter got his time down to a 1m39.502s this time as he led Honda team-mate Dani Pedrosa.ractice at Indianapolis.
The latter had a muted start to the day as he admitted he was still stiff from recent injuries in practice one.
But he was straight up to speed in the second session and for a while was half a second quicker than the rest.
His 1m39.582s was reeled in by the rest though, with third-placed Stefan Bradl getting to within 0.099s.
Jorge Lorenzo could only manage fourth, 0.253s off the pace on the best Yamaha.
His stablemates Cal Crutchlow and Valentino Rossi completed the top six, just ahead of Alvaro Bautista. Rossi had a brief off at Turn 13 late on.
Bradley Smith was eighth, followed by the two factory Ducatis.
Aleix Espargaro was top CRT man in 11th.
Karel Abraham was cleared to continue after his violent morning accident and was 22nd. He did not sustain any broken bones, though he did damage muscle in his shoulder.
Bradl had a minor fall early in practice two, with Hiroshi Aoyama also crashing later on.
But the only actual interruption was a red flag for a displaced marker cone on the approach to Turn 1.