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.