French rider Johann Zarco will line up behind the two factory Yamahas in third place for the privately-run Tech3 Yamaha team at the Bugatti circuit in his first top three start.
One tenth of a second divided the top two, with Vinales setting the best lap time of one minute 31.994 seconds and Rossi 0.106 slower.
It was the Spaniard's first proper MotoGP pole after the season-opener in Qatar, which was decided on practice times due to bad weather.
Britain's Cal Crutchlow was fourth on the non-works LCR Honda and ahead of the factory bike ridden by Spain's reigning world champion Marc Marquez. Ducati's Italian rider Andrea Dovizioso completed the second row.
Australian Jack Miller was lucky to survive unscathed from a massive crash in final practice, with his Marc VDS Honda going off track and slamming into the tyre wall. He returned to qualify 11th.
Rossi leads Vinales in the standings by two points after four races with Marquez a further two behind.
(Reporting by Alan Baldwin in London, editing by Ken Ferris)
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