In a frantic final 15 minutes, pole position changed hands frequently as Ducati, Aprilia and KTM battled for top honours.
A late 1m28.539s from reigning world champion Bagnaia moved him to top spot and allowed him to take his fifth pole of the season.
Vinales was second from KTM’s Brad Binder to complete the front row, as Fabio Quartararo was the sole Japanese manufacturer representative in the top 10, qualifying ninth on his factory Yamaha.
With a new circuit lap record set on Friday in practice, the battle for pole was expected to be a frantic affair, and proved so in the opening salvo.
Aprilia’s Aleix Espargaro set the initial pace at 1m29.916s, before Binder – who has signed a new contract with KTM through to the end of 2026 – edged ahead with a 1m29.610s.
But Binder’s lap was scrubbed for exceeding track limits, reinstating Espargaro to the top of the order before RNF Aprilia’s Miguel Oliveira took over with a 1m29.807s.
Vinales then set the pace with a 1m29.249s with just under 11 minutes to go, before Binder edged ahead with a 1m29.206s.
With nine minutes remaining, Vinales set a new reference with a 1m28.907s as nine minutes remained, after team-mate Espargaro crashed at Turn 3 seconds earlier.
Vinales’ time stood as the benchmark until the final three minutes, when he found a 1m28.576s.
But a first pole for Aprilia was denied by Bagnaia, who edged ahead by 0.037 seconds with his final flying effort of 1m28.539s – albeit missing out on a new lap record by just 0.006s.
Vinales held onto second, while Binder completed the front row for the first time since last year’s Japanese GP.
Source: Autosport