As Lorenzo's Yamaha dominated from the front, a resurgent Rossi thrived in the adverse conditions and was always in the fight for the podium.
Having finally broken clear of Tech 3's Andrea Dovizioso and Cal Crutchlow, Rossi began to rapidly close down Stoner and spent the final five laps swarming over the back of the reigning world champion's Honda.
Twice he got through only for Stoner to immediately re-pass him, but on the final lap he dived down the inside at the first chicane and made the move stick, pulling away over the remainder of the lap to seal second.
Stoner's loss boosted Lorenzo yet further: trailing the Australian by one point coming into Le Mans, he now leads by eight.
Lorenzo was effectively in a race of his own from the very start, as an aggressive opening lap gave him a near-two second advantage. He pulled away further as the race progressed, and - save for a small rally from Stoner, when the gap began to fall - was never troubled.
With poleman Dani Pedrosa (Honda) falling back, Stoner initially occupied second ahead of Rossi, Dovizioso and Crutchlow.
The Australian managed to edge away as the three behind him began fighting, with Crutchlow moving into third seven laps in. Dovizioso followed him through, but after biding his time for a few laps Rossi moved back into third and began hunting down Stoner.
Both Dovizioso and Crutchlow fell while trying to stay with Rossi, but were able to get back up and finished seventh and eighth respectively.
Their falls promoted Pedrosa to fourth, LCR Honda's Stefan Bradl into fifth and Rossi's Ducati team-mate Nicky Hayden into sixth.
Behind the Pramac Ducati of Hector Barbera and the Gresini Honda of Alvaro Bautista, Paul Bird's James Ellison triumphed from a three-way battle with Danilo Petrucci (Ioda-Aprilia) and Mattia Pasini (Speed Master Aprilia) to finish top of the CRT pile in 11th.
As Lorenzo dominated out front, the second works Yamaha of Ben Spies endured a torrid race.
A wobble at the start dropped him down the field and he never recovered, even pulling into the garage at the halfway mark before returning at the back of the pack.