A 1m41.697s from Leclerc amid the first runs in the eight-minute SQ3 session proved unassailable, and a second set of laps from both Perez and Verstappen could not topple the Monegasque's searing pace around the Baku circuit.
The Red Bull duo were especially keen to be first out in the final part of qualifying, sitting at the pitlane exit for a few minutes between sessions, and immediately began proceedings with the initial headline efforts.
Perez posted a 1m41.876s to go top, and Verstappen was unable to beat his team-mate's effort having complained that he "lost all the rear in the middle sector".
Leclerc reprised his form from Friday and fired his Ferrari across the line with a 1m41.697s to sit on top of the order, once again throwing down the gauntlet to Red Bull.
Although Perez began to hit back, setting the best middle sector time of the session and threatening to usurp Leclerc, he was unable to make the difference in the final sector and crossed the line 0.15s shy of Leclerc's benchmark.
Attempting to better his own time, Leclerc then gave the Ferrari garage a scare by putting his Ferrari into the barrier at Turn 5, but only damaged his front wing and was able to back it out of the wall - compromising team-mate Carlos Sainz's lap in the process.
Verstappen improved his time but was unable to claim any ground on Leclerc and Perez, and will thus start the sprint race from third on the grid.
With Sainz unable to make any gains, George Russell moved past the Spanish driver to claim fourth on the grid for the shortened Saturday race. His team-mate Lewis Hamilton starts from sixth, alongside Sainz on the third row.
Having carried his Williams all the way to SQ3, Alex Albon will start the sprint from seventh ahead of Fernando Alonso, who was suffering amid continued DRS issues at Aston Martin. Lance Stroll was ninth quickest, while Lando Norris could not run in SQ3 having had no sets of soft tyres left.
The rules dictate that a fresh set of softs must be used, but McLaren decided to sacrifice a potential SQ3 outing on Friday and employed that set during his Q3 lap - giving him seventh on the grid for Sunday's race.
Oscar Piastri was unable to progress to the final part of qualifying, despite getting into the top 10 late on in SQ2 with a lap 0.03s shy of team-mate Norris.
But Stroll received a tow from Alonso in a showing of great teamwork among the Aston Martins, slingshotting the Canadian into the top 10 at Piastri's expense.
Nico Hulkenberg overcame a near-miss with the wall at Turn 7, where he sustained a lock-up at the front, to shuffle up to 12th as Haas did not have the pace to provide a concerted challenge for SQ3.
Esteban Ocon could only go 13th fastest in a difficult session for the Alpine squad, albeit three tenths clear of Kevin Magnussen.
With 30 seconds left on the clock of SQ1, Logan Sargeant hit the wall at Turn 15 to effectively freeze the order for the opening 12 minutes of running, breaking the right rear corner of his Williams in the process.
Sargeant had been 11th fastest, but could take no further part in the session given the extent of the damage - the American citing that the "Ferraris were in the middle of the road" on the exit of the Old City section.
This denied the Alfa Romeos of Zhou Guanyu and Valtteri Bottas a chance to break out of the bottom five. But the timing of the red flag was more cruel for Yuki Tsunoda, who had qualified in the top 10 for Sunday's grand prix, and was on course to better his lap before the session was stopped as he was on the final straight.
Pierre Gasly entered the pits after his initial runs, and thus could do no better than 19th on the grid - and was only spared from the bottom of the pile by Nyck de Vries. The Dutchman endured a troubled run, once more going deep at Turn 3 - but this time, avoided the wall and managed to reverse out.
F1 Azerbaijan GP - Sprint qualifying results
| Cla | Driver | Chassis | Engine | Time | Gap | |
|---|---|---|---|---|---|---|
| 1 |  Charles Leclerc |
 |
Ferrari | Ferrari | 1'41.697 | |
| 2 |  Sergio Perez |
 |
Red Bull | Red Bull | 1'41.844 | 0.147 |
| 3 |  Max Verstappen |
 |
Red Bull | Red Bull | 1'41.987 | 0.290 |
| 4 |  George Russell |
 |
Mercedes | Mercedes | 1'42.252 | 0.555 |
| 5 |  Carlos Sainz |
 |
Ferrari | Ferrari | 1'42.287 | 0.590 |
| 6 | Lewis Hamilton |
|
Mercedes | Mercedes | 1'42.502 | 0.805 |
| 7 |  Alex Albon |
 |
Williams | Mercedes | 1'42.846 | 1.149 |
| 8 | Fernando Alonso |
 |
Aston Martin | Mercedes | 1'43.010 | 1.313 |
| 9 |  Lance Stroll |
 |
Aston Martin | Mercedes | 1'43.064 | 1.367 |
| 10 | Lando Norris |
 |
McLaren | Mercedes | ||
| 11 |  Oscar Piastri |
 |
McLaren | Mercedes | 1'43.427 | 1.730 |
| 12 |  Nico Hulkenberg |
 |
Haas | Ferrari | 1'43.806 | 2.109 |
| 13 |  Esteban Ocon |
 |
Alpine | Renault | 1'44.088 | 2.391 |
| 14 |  Kevin Magnussen |
 |
Haas | Ferrari | 1'44.332 | 2.635 |
| 15 |  Logan Sargeant |
 |
Williams | Mercedes | ||
| 16 |  Zhou Guanyu |
 |
Alfa Romeo | Ferrari | 1'45.177 | 3.480 |
| 17 |  Valtteri Bottas |
 |
Alfa Romeo | Ferrari | 1'45.352 | 3.655 |
| 18 |  Yuki Tsunoda |
 |
AlphaTauri | Red Bull | 1'45.436 | 3.739 |
| 19 | Pierre Gasly |
 |
Alpine | Renault | 1'46.951 | 5.254 |
| 20 | Nyck de Vries |
 |
AlphaTauri | Red Bull | 1'48.180 | 6.483 |
| View full results | ||||||
