The Red Bull driver enjoyed a drag lift through the last sector and delivered a mighty 1: 09.623 seconds, which was the only lap to break the 1: 10s limit, and ran a full 0.0556s flawlessly at the top.
Bottas was the closest challenger at Zandvoort thanks to his 1: 10.179-minute lap, although that was enough to beat Hamilton’s best performance by 0.24 seconds.
Robert Kubica, who replaces Kimi Raikkonen at Alfa Romeo after a positive COVID test for the 2007 champion, was the first driver on the track in front of Nikita Mazepin’s Haas.
Kubica led his car, which was strapped on the fastest soft C3 Pirelli tires, to a time of 1: 15.854 minutes to get the early benchmark as Mazepin ran 0.076 seconds slower on the C2 yellow wall compound.
The soft-tire Schumacher then reduced this to 1: 14.099 minutes after four minutes and ran 1.755 seconds ahead of early runner Yuki Tsunoda for AlphaTauri.
After his oil stop at the beginning of FP2 due to the oil supply, Hamilton quickly left the garage and moved up to the front of the field with his 1: 12,010 minutes on soft tires.
He was dropped off by Alonso after 14 minutes, with the Alpine racer reducing the pace to 11,996 minutes on medium-sized tires before falling behind Hamilton, who completed a second run.
The Mercedes driver ran flawlessly in just under 0.032 seconds, but his two runs were hindered by small mistakes.
Hamilton dropped his left front wheel onto the gravel inside the Turn 12 sweeper before stalling and running across the grass during his second stint.
Ferraris’ brace kicked off after 13 minutes, with Leclerc leading his medium-tire machine in 1: 11.768 seconds on his first attempt to find 0.196 seconds over Hamilton.
FP2 pacesetter Leclerc was assisted by Carlos Sainz before the pair was split by McLaren’s Lando Norris and Alonso ran the fastest again with 1: 11.705 minutes to find a pad of 0.063 seconds.
Sainz soon raised the red flags in the three practice sessions when he broke off the procedure after 20 minutes with significant damage to the front and left rear of the car.
The Ferrari driver, who was second fastest in FP2 behind Leclerc, lost the rear end of the bend in Turn 2 and then jumped into the Tecro barrier that lined the top of the embankment of Turn 3.
Before the interruption, Valtteri Bottas had just started his out-round, while Verstappen did not have to leave the box and only entered the session after 33 minutes.
Verstappen eventually started a run on midsize tires when he shared the track with a soft Bottas, and it was the Red Bull driver who took the lead with a banker of 1: 11.225s.
But Bottas reacted immediately to the faster compound and freed 0.008 seconds and headed straight for the pits, while Verstappen stayed on the way to improve his time.
That paid off when the Dutch racing driver stormed below the threshold of 1:11 for the first time with a time of 1: 10.702 minutes, widening a solid gap of half a second in his favor.
Norris moved up to second place but was still 0.417 seconds behind him before Alonso once again made it to the top of the leaderboard on the soft tires thanks to his flying lap of 1: 10.670 minutes.
The changes to the front line were interrupted by a yellow flag at Turn 9 where Norris suffered an episode of snap oversteer at the apex and walked over the gravel.
Bottas then showed up on Softs to run fastest at one minute, 10.179 seconds to find a chunky five-tenths swing over Alonso, while Hamilton was provisional second as he lapped 0.238 seconds slower.
As the session went into the last 10 minutes, Verstappen made his way to a penultimate run on the soft tires and drove the fastest time in all three sectors, partly supported by a slipstream through the last part of the lap Weekend to achieve.
Behind Bottas and Hamilton, 0.794 seconds behind the pace, Perez ran into fourth place, while Alonso was eventually pushed back to fifth ahead of Norris.
Lance Stroll led Aston Martin’s attack in seventh place, dwarfing teammate Sebastian Vettel while Leclerc defeated Gasly in the fight on the edge of the top 10.
Ricciardo, who suffered a sizable suspension early on at Turn 1, finished 11th ahead of Nicholas Latifi, Esteban Ocon and Spa podium finisher George Russell.
Antonio Giovinazzi ran for Alfa Romeo in 15th place ahead of Sainz and was 0.9 seconds ahead of the returning Kubica.
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