Hayden had been an almost identical 1.136s from the top on the last day of pre-season testing at the track, when he was riding soon after wrist surgery.
“It hasn't been an easy day,” said the American on Saturday. “In qualifying I lost some time due to a couple of issues I was having with the clutch and rear brake.
“Then we made a few little changes and got going better, but I had so much chatter that both of my hands are still tingling. I think a lot of guys are dealing with it, but it's really making it difficult for me in the fast corners.
“I was able to do an okay lap, but the pace is really fast. I made one little mistake on what turned out to be my best lap, and that probably cost me two or three tenths.
“We've got a couple decisions to make for tomorrow, and we'll see what we can do.”
Both Rossi and Hayden fell at turn one in Saturday morning's final practice. The #46, winner at Sepang in 2010, is to return to Yamaha next season.