The Aprilia rider set a time of 1 minute 19.622 seconds, to end the day 0.340sec ahead of compatriot and championship leader Jorge Martin on a Ducati-Pramac. Portuguese rider Miguel Oliveira of Aprilia satellite team Trackhouse was a further 0.022sec behind in third.
Reigning champion, Francesco Bagnaia, who is just 10 points behind Martin after winning both the sprint and the main race in Assen last week, was fifth on his Ducati.
Six-time world champion Marc Marquez, who is third in the overall standings, finished only 13th after going over the handlebars of his Ducati-Gresini and wrecking his first-choice bike.
The ten fastest on Friday go straight to Saturday's final qualifying session, known as Q2.
As such, Marc Marquez will have to finish in the top two in Q1 in order to advance to Q2 and fight for a place on the first four rows of the grid.
The Spaniard was examined at the track medical centre and doctors found he had a broken left index finger and a "large bruise to the ribcage", but declared him "fit" to continue racing on a track where he is chasing a record ninth victory.
Italian Fabio Di Giannantonio was also the victim of a fall in practice. His Ducati-VR46 ended up in the inflatable protection installed around the circuit and the accident interrupted the session for around 10 minutes, while the damage barriers were repaired.
Augusto Fernandez, Takaaki Nakagami and Marco Bezzecchi also crashed.
Australian Jack Miller of KTM will have to ride in Q1 after finishing 11th, one thousandth of a second slower than South African team-mate Brad Binder.
One rider who enjoyed a less happy day was the second Aprilia rider, Aleix Espargaro, who withdrew after attempting to practise with a fractured right little finger which he broke at Assen.
"It's on the right hand, which I use to accelerate but I didn't want to stay at home," Espargaro told the MotoGP site. "So, I came here, I tried my best but it's impossible, I am in a lot of pain."
