As was the case across Friday practice, Misano's track conditions once again existed in that fine area just between slicks and wets.
Unlike Friday however there was at least action from the outset, with all of the prototype riders choosing to run ahead of a qualifying session that could mirror the morning environment.
Title rivals Dani Pedrosa and Jorge Lorenzo traded top spot as the session wore on, but in the final minutes Gresini's Bautista went fastest with a 1m42.393.
While that was still not faster than Karel Abraham's benchmark from Friday, it was nevertheless a welcome boost for the only prototype rider yet to have his ride confirmed for next year.
At the flag Rossi, who made the bold decision to switch to slicks in the final six minutes, improved to second. He was however more than one second down on Bautista.
That pushed Lorenzo down to third, with Pedrosa half a second down the road in fourth.
Tech 3's Andrea Dovizioso was fifth, with the variable conditions and low track temperature helping Danilo Petrucci to finish as the top CRT rider in sixth.
Stefan Bradl emerged from the pitlane in the final 20 minutes to go seventh fastest, ahead of CRT duo Michele Pirro and Aleix Espargaro and the second works Ducati of Nicky Hayden.