The Mexican driver bolted to the top with his final flying lap of Q3 on the Jeddah Corniche Circuit as he romped to a weekend-best 1m28.200s to triumph over the strong Ferraris.
That meant the late improvement of Leclerc, as the free practice pacesetter finally had an answer to Sainz in qualifying, missed out on consecutive pole positions by just 0.025s.
Sainz, who had headed the leader board after the first runs in the Q3 10-minute dogfight, could not put together one final flier and so slipped to third by two tenths compared to his teammate.
A messy Q3 showing for defending champion Max Verstappen returned fourth place, with the Red Bull driver struggling initially in Q3 as he battled oversteer while applying the throttle out of Turn 2.
Esteban Ocon ran to fifth for Alpine as the French car and driver combination dropped eight tenths to the leaders but pipped Mercedes driver George Russell and Fernando Alonso.
Russell executed an off-beat strategy by leaving his best effort for the mid-point of the session rather than engage in a last-ditch shootout over the line.
The Briton clocked a 1m29.104s to land sixth over Fernando Alonso and the Alfa Romeo of Valtteri Bottas. Pierre Gasly and the Haas of Kevin Magnussen completed the top 10 runners.
Russell was the only Mercedes-powered contender to move into the top 10 shootout after Daniel Ricciardo and his McLaren teammate Lando Norris failed to hook up an improved lap in the massively delayed Q2 fight.
A huge shunt for Mick Schumacher forced the 15-minute session to be put on ice for 57 minutes while the Haas driver was taken to hospital after an initial check at the medical centre revealed no injuries.
This came after the German ran wide out of Turn 10 over the exit kerb and on the slippery surface, the VF-22 swapped ends and Schumacher ran nose first into the wall at high speed.
As per new crash structure designs, when the car was craned, the rear end split from the main chassis to cause a further clear up delay in addition to the track needing cement dust and a steam blast before FIA race director Niels Wittich was satisfied with his inspection.
With a little under five minutes to run, late climbers were few and far between.
But the second Haas of Kevin Magnussen and Esteban Ocon – who was delayed by Ricciardo in an incident that remains under investigation - made it through in eighth and ninth.
That left Russell prey as Gasly improved to seventh, but Ricciardo could not whittle down his personal best to survive while Zhou Guanyu only climbed his Alfa Romeo to 13th.
Norris was out in 11th ahead of Ricciardo, Zhou and Schumacher - ninth at the time of his crash - over Lance Stroll.
Hamilton, meanwhile, was the first driver to miss out on progressing into the second part of qualifying after his final flying lap was 0.087s slower than the cut off set by Stroll.
The seven-time champion was only 16th fastest in Q1 after initially losing the rear end of his Mercedes W13 challenger with a snap of oversteer at Turn 2 on his first flying soft-tyre run.
After beginning the Saturday evening session on the medium compound alongside Russell only, Hamilton was forced into a final push lap with a minute to spare in order to progress.
However, the lap started off the pace when the Brit was adrift of his personal best throughout sector two on his way to a 1m30.343s.
Despite a better sprint to the finish to initially move 15th, Stroll was next over the line to bump Hamilton out in Q1 for the first time since he crashed in Brazil qualifying in 2017.
He was only faster on merit than the Williams of Alex Albon and Aston Martin's substitute driver Nico Hulkenberg, the pair dashing to 17th and 18th respectively.
Meanwhile, Nicolas Latifi crashed out to bring the red flags into play after seven of the 18 minutes when the rear of his FW44 snapped out of control at Turn 13.
The Canadian appeared to immediately lose the back axle when he turned in, glancing the barrier before landing in the outside wall.
Yuki Tsunoda was unable to set a lap either side of the eight-minute delay owing to a fuel issue for the AlphaTauri, which arrived in Saudi with a fresh power unit.
| Cla | Driver | Chassis | Engine | Time | Gap | |
|---|---|---|---|---|---|---|
| 1 |  Sergio Perez |  | Red Bull | Red Bull | 1'28.200 | |
| 2 |  Charles Leclerc |  | Ferrari | Ferrari | 1'28.225 | 0.025 |
| 3 |  Carlos Sainz Jr. |  | Ferrari | Ferrari | 1'28.402 | 0.202 |
| 4 |  Max Verstappen |  | Red Bull | Red Bull | 1'28.461 | 0.261 |
| 5 |  Esteban Ocon |  | Alpine | Renault | 1'29.068 | 0.868 |
| 6 |  George Russell |  | Mercedes | Mercedes | 1'29.104 | 0.904 |
| 7 | Fernando Alonso |  | Alpine | Renault | 1'29.147 | 0.947 |
| 8 |  Valtteri Bottas |  | Alfa Romeo | Ferrari | 1'29.183 | 0.983 |
| 9 | Pierre Gasly |  | AlphaTauri | Red Bull | 1'29.254 | 1.054 |
| 10 |  Kevin Magnussen |  | Haas | Ferrari | 1'29.588 | 1.388 |
| 11 | Lando Norris |  | McLaren | Mercedes | 1'29.651 | 1.451 |
| 12 |  Daniel Ricciardo |  | McLaren | Mercedes | 1'29.773 | 1.573 |
| 13 |  Zhou Guanyu |  | Alfa Romeo | Ferrari | 1'29.819 | 1.619 |
| 14 |  Mick Schumacher |  | Haas | Ferrari | 1'29.920 | 1.720 |
| 15 |  Lance Stroll |  | Aston Martin | Mercedes | 1'31.009 | 2.809 |
| 16 | Lewis Hamilton |  | Mercedes | Mercedes | 1'30.343 | 2.143 |
| 17 |  Alex Albon |  | Williams | Mercedes | 1'30.492 | 2.292 |
| 18 | Nico Hulkenberg |  | Aston Martin | Mercedes | 1'30.543 | 2.343 |
| 19 | Nicholas Latifi |  | Williams | Mercedes | 1'31.817 | 3.617 |
| 20 |  Yuki Tsunoda |  | AlphaTauri | Red Bull | ||
| View full results | ||||||
