The Red Bull driver and local favorite appeared to have been overshadowed by a last-second Ferrari threat that culminated after two red flags in Q3 caused by Lewis Hamilton and then George Russell.
With defending champion Verstappen wasting time through the first half of the lap on his final run, Leclerc might have taken the lead when he crossed the line to move into first place.
But Verstappen knocked him out of the bag as he clawed back lost ground in the final sector to score what could have been an unlikely pole. He was the only pilot to dive in the 1m04.
Indeed, the qualifications were summed up in the 2m30 finals following the falls of Mercedes.
Verstappen’s Q3 banker had him provisionally fastest as he left the Red Bull Ring pits behind the two Ferraris.
Leclerc was first across the line to start his final push for pole, only to lose a tenth in the first sector to Verstappen.
But he recovered that with a fastest overall final sector, while Verstappen was apparently behind.
Leclerc therefore jumped to the top of the standings with an effort of 1m05.013s.
Sainz was a little adrift with a 1m05.066, completed by three personal best sectors, which appeared to have cemented pole for Leclerc.
But Verstappen then pulled out a personal best in the final sector that was enough to make up for the damage earlier in the lap and he soared in 1m04.984s to grab a remarkable 0.19s sprint pole run.
Sainz will be joined on the second row of the grid by Sergio Perez as Russell’s effort before the accident was enough for fifth ahead of Esteban Ocon.
Kevin Magnussen finally got his legs on Haas team-mate Mick Schumacher to end a close team feud in seventh, while Fernando Alonso was ninth.
Hamilton, meanwhile, was relegated to 10th place due to his incident in the first half of the final 10-minute qualifying game.
In the first of the Mercedes shunts, Hamilton pulled out the red flags in Q3 with 5m29s to go after crashing into the barrier at Turn 7.
The seven-time champion, who had just oversteered on the exit of Turn 6, was slightly off the apex, causing the rear of his Mercedes W13 to lose control.
Hamilton was quick to correct him, but as the car clung, the applied steering lock threw him off the road and through the gravel.
He rammed the wall sideways to break the right front and back corners.
The shunt was met with cheers from the Dutch crowd, with Hamilton a credible threat in the front row after leading the times for much of Q2 as he cut his time to 1m05.475s before being relegated in third place behind Leclerc and Verstappen. .
After the 11-minute break, Russell followed Alonso out of the pits to enjoy the fresh air as he looked to improve on his fifth fastest effort.
But despite the uneventful run, he ran slower than his personal best in the first sector to sit 0.42 seconds off Verstappen’s benchmark before flashing a second sector green.
Then, much like his teammate, Russell lost the rear in the final turn as he broke too hard to swing Russell towards the outside wall of the tire, ultimately crumpling his rear wing.
Russell remains under investigation for entering the track without permission at Turn 10 while crossing the track under the red flag to return to the Mercedes garage.
Perez could also create new controversy. The Monaco GP winner had a shot at moving up to Q3 after various track limit violations had his lap times scrapped.
He then progressed into the latter part of qualifying on his final attempt, finishing Q2 in sixth, only to be noted for crossing the white lines at the left-right transition through the open corner chicane 7-8 after the end. of the session and positions 11-15 decided.
Norris was the main victim of Q2, having finished the first part of qualifying in eighth, despite going off the road at turn 3, to massively put his teammate Ricciardo in the shade.
But the driver who caused the first of two red flags in FP1 after reporting smoke under his seat then found himself last in Q2 as the boiling Briton was “afraid to hit the brakes”.
The McLaren driver started the 15-minute dice by oversteering at Turn 3 before enduring masses of understeer at Turn 4 to cut the gravel and have his lap time suppressed.
On his next attempt, he ran far into turn 1 and had to abandon the turn.
This left him last and without time as he then missed three of the seven defined corners, although the FIA recognizes 10 corners.
He locked in at turn 3 and turn 4 before scoring the kitty litter again on the exit of turn 6.
Norris had one possible last attempt but stopped to finish the session 15th.
Further ahead thanks to a time of 1m06.160, Pierre Gasly was the first driver to miss Q3.
He spun around 0.11s slower than Schumacher to set the 11th fastest time ahead of Alex Albon’s improved fast Williams FW44 and Valtteri Bottas’ Alfa Romeo.
Yuki Tsunoda ran 14th, having ruined his last attempt by sliding at Turn 1 – which was met with anger over the team radio by rider AlphaTauri.
Ricciardo’s difficult season and uninspiring form at Silverstone lingered as he became the first person to miss Q2, with the Aussie missing the cut by 0.024s.
While his teammate Norris finished the first 18-minute part of qualifying in eighth, despite crashing out at Turn 3, Ricciardo only managed 16th to lose to Gasly’s AlphaTauri.
Meanwhile, Lance Stroll had appeared poised to progress in the second part of qualifying, racing in the top 15 for much of the opening gambit, only to slip to 17th.
Stroll was a multiple track limit violator, running wide at Turn 10 – the final corner – to have his current and next lap cleared before pushing his luck at Turn 1.
He has consistently edged Zhou Guanyu’s Alfa Romeo, while Nicholas Latifi took the former Williams to 19th ahead of four-time champion Sebastian Vettel.
The Aston Martin driver had initially spun faster than his team-mate only to be sent down the lap times when he overshot the track limits at Turn 10 to have his time removed.