The Mercedes driver, who has won eight Hungarian Grand Prix, is now a step closer to a landmark 100th grand prix victory following a superb qualifying performance at the Hungaroring.
Verstappen had secured the last four pole positions but he had to settle for third behind an all-Mercedes front row as Hamilton netted his first pole in six races since the Spanish Grand Prix.
Hamilton posted a time of one minute 15.419s, with team-mate Valtteri Bottas over three-tenths of a second adrift, while Verstappen was a further tenth back.
There was a bone of contention at the end of Q3, however, as a slow train of cars, with Hamilton, Verstappen and Perez at the rear of the nine on track, resulted in the Mexican failing to get across the line in time to set another quick lap.
Hamilton, in particular, appeared to hold up the two Red Bull drivers behind him. Perez will at least start fourth ahead of AlphaTauri's Pierre Gasly.
A strategy battle will unfold in the race as well, as Verstappen and Perez will start on the soft tyre while Hamilton and Bottas will be on the medium compound, the latter seemingly offering the better run plan.
Verstappen had sat on the cusp after his opening medium-tyre run in Q2 and due to the track ramping up in terms of grip as the session wore on as temperatures hit 60 degrees centigrade, forcing the team to send him out on the soft tyres.
With six minutes 40 seconds of Q2 remaining, Carlos Sainz brought out the red flags at a point when he appeared on course to secure a place in the top 10.
Sainz, who had finished fourth quickest at the end of Q1, lost control of his SF21 as he turned into the final corner, sliding full-lock across the run-off area and smacking into a tyre wall with the left-hand side of the car.
Although Sainz managed to pull away, he quickly lost and ran over his front wing, forcing him to stop and be retrieved by the marshals, leaving him to start 15th.
Ahead of the Spanish driver after their own Q2 exits will be Daniel Ricciardo in his McLaren after another troubled session.
At the end of Q1, Ricciardo was only 14th fastest, finishing six-tenths of a second behind team-mate Norris, while half-a-second separated the duo in Q2 in which the Briton was second quickest.
Exiting Q1 were AlphaTauri's Yuki Tsunoda who starts 16th, potentially as a consequence of missing all but the last couple of minutes of FP2 after crashing in the first practice session.
For the first time this season, George Russell failed to make it out of Q1 and will start 17th ahead of team-mate Nicholas Latifi, with the Briton claiming he "couldn't get the car working".
On the back row will be Haas duo Nikita Mazepin and Mick Schumacher, the latter unable to take part in the session as the team failed to carry out repairs in time after his heavy crash into a tyre wall in FP3.
GPFans is a multi-platform, multi-language brand dedicated to Formula One coverage. We bring you all the ins and outs of the sport, 24/7, everything from up-to-the-minute news and features to the latest viral stories and clips.
We believe that a new generation of exciting, outspoken drivers will make F1 more popular than ever before, and we want to give our users access to as much of their heroes as possible, on and off the track. From Lewis Hamilton to Max Verstappen, Daniel Ricciardo to Sebastian Vettel, we provide in-depth analysis of every every Grand Prix in the season, from Australia to Abu Dhabi.
With Formula One under the new ownership of Liberty Media, how the sport is being covered is evolving, and GPFans will look to be at the heart of this progression into new media, as one of the fastest-growing sites covering the king of motorsports.