Although a dry line quickly emerged during the 20-minute session, no riders used slick tyre, with the medium-compound wet tyre proving the rubber of choice for most riders.
Vinales became the first rider to breach the two-minute barrier with a little over a minute to go when he posted a 1m59.524s, knocking KTM’s Mika Kallio off the top spot.
Crutchlow then grabbed the top spot with a 1m59.400s aboard the LCR Honda, before Vinales responded with a final effort of 1m59.111s to go 0.289s clear.
Joan Mir was third for Suzuki, 0.403s off the pace, ahead of another rookie, Francesco Bagnaia on the Pramac Ducati, while Valentino Rossi was the only other rider to set a time in the 1m59s in fifth on the second works Yamaha.
Kallio was sixth ahead of Crutchlow’s teammate Takaaki Nakagami and Alex Rins’ Suzuki.
Front-row starter Fabio Quartararo ended up down in 17th, more than four seconds off the pace, while poleman Marc Marquez was one of four riders not to set a timed lap.