Dani Pedrosa edged out title rival Jorge Lorenzo to set the pace as wet track conditions persisted in the final practice session at Aragon.
The Honda rider made his move in the final two minutes of the session, dropping down to a 2m00.490s.
That was enough to edge out Yamaha's Lorenzo, who had been top since the halfway mark, by just over one tenth of a second.
Ben Spies on the second works Yamaha backed up his chart-topping FP2 pace by claiming third, fractions ahead of the satellite Tech 3 bike of Andrea Dovizioso.
LCR Honda's Stefan Bradl meanwhile claimed fifth, just one thousandth of a second ahead of the second Tech 3 of Cal Crutchlow.
The Briton's session was brought to a premature close when he fell at Turn 12 seven minutes from the end.
Karel Abraham on the satellite Cardion Ducati also fell early on, as track temperatures dropped to a weekend-low.
He was able to return however and climb to seventh, ahead of Ducati's Valentino Rossi.
Team-mate Nicky Hayden finished 10th, just over one tenth of a second down on the second works Honda of Jonathan Rea.