The hour-long qualifying group-deciding session proved to be a tense affair, with just 0.673 seconds covering the top 10.
Bagnaia set the pace with a 1m31.340s, posted with just over 10 minutes to go, and proved strong enough for the world champion to box early at the end of the session.
Apriliaās Vinales challenged him for top spot at the end but came up just 0.065s short as team-mate Aleix Espargaro suffered a nasty highside at the final chicane.
This incident brought out yellow flags and scuppered the final laps of a number of names, with the most notable Q1 entries proving to be Yamahaās Fabio Quartararo and Tech3 GasGas rookie Pedro Acosta.
Alex Marquez leapt up to third late on for Gresini Ducati, while Espargaro was fourth despite his crash ahead of championship leader Jorge Martin, who was involved in an odd incident with Jack Miller in the closing stages.
Martin was riding slowly on the racing line through the Turn 9 left-hander, while KTMās Miller was looking behind when he went through the corner.
Looking around at the last moment, Millerās head made contact with Martinās back and his KTM suffered some aerodynamic damage ā but both stayed on their motorcycles.
Pedro Acosta, Red Bull GASGAS Tech3
Photo by: Gold and Goose / Motorsport Images
Marc Marquez was sixth on the second Gresini Ducati, with KTMās Brad Binder seventh ahead of Ducatiās Enea Bastianini ā who crashed at the end of the session.
Trackhouse Racingās Raul Fernandez continued his strong Friday at Assen in ninth on his 2023-spec Aprilia, while Franco Morbidelli took the final direct Q2 qualifying spot in 10thĀ on the sister Pramac Ducati.
Despite running Yamahaās new engine, which was met with rave reviews from Quartararo and Alex Rins in a recent private test, 2021 world champion Quartararo could do no more than 11thĀ in second practice.
Both VR46 Ducatis have also missed the Q2 cut in 12thĀ and 13th, Marco Bezzecchi heading Fabio Di Giannantonio, while Rins was 14thĀ from Acosta in 15th.
Top Honda honours went to Johann Zarco of LCR Racing in 17th, while Miller was left in 18thĀ after his scare with Martin.
MotoGP Dutch GP – FP2 results
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