The reigning world champion has won the Spanish GP for the past two years and comes into the 2024 edition off the back of two disappointing rounds in Portugal and America.
In a crash-strewn session, Bagnaia left it to the end of the hour to produce a 1m36.025s to lead the way by 0.100 seconds from Aprilia’s Vinales.
Marc Marquez looked on course to take top spot from Bagnaia at the end but came up just short with a 1m36.168s to move ahead of Marco Bezzecchi and championship leader Jorge Martin.
The Pramac rider set the early pace in the hour-long afternoon session at Jerez with a 1m37.811s, trading top spot with KTM’s Brad Binder before the South African edged clear with a 1m36.794s inside the first 10 minutes.
Then followed a period of several crashes in quick succession, with Bezzecchi, Raul Fernandez (Trackhouse Racing) and Vinales (Aprilia) sliding off.
Just over halfway into the session, Yamaha’s Fabio Quartararo came off his bike at Turn 7, with Alex Marquez (Gresini Ducati), Dani Pedrosa (KTM) and Miguel Oliveira (Trackhouse) also suffering falls.
With just over 20 minutes remaining, Vinales pushed for an early soft tyre run on his Aprilia and produced a 1m36.482s.
Photo by: Gold and Goose / Motorsport Images
This was beaten by Martin with a 1m36.435s about eight minutes later, before Vinales returned his Aprilia to the top of the times with a 1m36.125s.
This lap put Vinales underneath the existing lap record, but it would be bested by 0.100s by Bagnaia on his final flying lap at the end of the session.
Gresini’s Marc Marquez completed the top three from Bezzecchi, Martin and Tech3 rookie Pedro Acosta – who was the only KTM rider to make it into Q2 qualifying directly.
A costly crash for Binder in the closing stages left him at the fringes of the top 10 and eventually shuffled down to 11th when the field shook itself out.
Aleix Espargaro was seventh on the sister factory Aprilia, with Ducati’s Enea Bastianini, VR46’s Fabio Di Giannantonio and Alex Marquez taking the final Q2 spots.
The rest of the KTM contingent in Pedrosa, Jack Miller – who crashed late on – and Augusto Fernandez (Tech3) will join Binder in Q1 on Saturday morning, as will Pramac’s Jorge Martin, both Yamahas and all five Hondas.