Mercedes drivers George Russell and Lewis Hamilton finished down in fourth and ninth place respectively.
In the only representative practice session of the weekend given its evening setting, the field headed out in unusually cool temperatures – 17°C air temperature – with a strong headwind blowing down the main straight at the Sakhir venue.
Haas driver Kevin Magnussen was the first driver to head out, running the yellow-walled medium tyres that all drivers bar McLaren's Daniel Ricciardo used for their initial FP2 laps.
Magnussen duly set the first place benchmark at 1m34.572s, which was soon beaten by Carlos Sainz as the Ferrari driver followed Magnussen through during the early running.
But Leclerc, running shortly behind his teammate, posted a 1m33.121s that stood as the top time until nearly the end of the opening 30 minutes of the one-hour session.
Hamilton and the Red Bull drivers were the last drivers to appear on the mediums, with the Mercedes driver having to wait in his garage as his team finalised last minute set-up changes that included switching him to the floor specification that teammate Russell used in FP1 earlier on Friday afternoon.
Hamilton complained his car was "still bouncing a lot" even with that switch and he also had a big lock-up on his opening flying lap on the mediums that sent him deep and nearly off track at the exit of the first corner.
He languished down the field at this stage, while the Red Bull pair – with Sergio Perez only joining the fray after the opening quarter had elapsed – ran over half a second adrift of Leclerc's best during their medium tyre running.
When 20 minutes had passed, the switch to the soft tyres for qualifying simulation running took place, led by Aston Martin pair Nico Hulkenberg and Lance Stroll.
They climbed the order as a result, but could not better Leclerc's time on the harder mediums – with the Monegasque's benchmark finally beaten by Alpine's Fernando Alonso on a soft tyre effort that yielded a 1m32.877s after 26 minutes had passed.
Sainz's first run on the softs did get him ahead of Leclerc's medium tyre time, but only just as he lost time in the final sector.
With his first run on the softs a minute after Alonso's time had come in, Leclerc roared back to the top spot with a 1m32.263s that featured then purple times in all three sectors.
Perez led Red Bull's efforts on the softs as the opening half hour ended, but he wound up 0.6s slower than Leclerc with a slow middle sector.
Just inside the session's second half, Verstappen went for his qualifying sim flier and beat Leclerc in the opening sector.
He shipped a fraction in the middle part of the lap but recovered enough time by the end to go fastest on a 1m31.936s that stood as the best time to the end of the session.
A few minutes later, Leclerc went for a second go on the softs and with a stronger final sector, although with a slower middle sector than his personal best, he closed to nearly match Verstappen's time.
Before that, the Mercedes drivers had posted their soft tyre efforts, with Russell leading the way, albeit 0.593s slower than Verstappen.
Hamilton had had to abandon his first flying lap on the softs after he locked up again at Turn 1 and went deep, the seven-time world champion reporting a "problem with the front brakes" that were "pulling" on his front-right corner, and Mercedes later explaining he was also losing out with a malfunctioning DRS.
Hamilton's soft tyre time was a 1m33.144 that ended up as the ninth fastest time, 1.208s behind Verstappen's best.
Sainz finished with the third quickest time as he was given another attempt on the softs early in the sessions final third, where the field switched to the traditional long-run data gathering for race preparations.
He jumped to finish 0.584s slower than Verstappen, but ahead of Russell and Alonso.
Valtteri Bottas recovered from his misfire-mangled FP1 to finish sixth with 29 laps completed for Alfa Romeo, ending up ahead of Perez and Mick Schumacher in the lead Haas.
Magnussen followed his teammate the other side of Hamilton in 10th place.
Lando Norris finished with the 11th fastest time ahead of Esteban Ocon, who was another driver reporting severe porpoising during the early running.
Ricciardo finished with the lowest lap count – 12 – as he sat out the end of the session as McLaren worked on the rear of his MCL36 in the pits.
Tsunoda, who finished 14th overall, with FP1 pacesetter Pierre Gasly 13th in the other AlphaTauri, also made contact with Stroll at the entry to Turn 8 during the closing stages.
| Cla | Driver | Chassis | Laps | Time | Gap | |
|---|---|---|---|---|---|---|
| 1 |  Max Verstappen |  | Red Bull | 20 | 1'31.936 | |
| 2 |  Charles Leclerc |  | Ferrari | 20 | 1'32.023 | 0.087 |
| 3 |  Carlos Sainz Jr. |  | Ferrari | 22 | 1'32.520 | 0.584 |
| 4 |  George Russell |  | Mercedes | 25 | 1'32.529 | 0.593 |
| 5 | Fernando Alonso |  | Alpine | 24 | 1'32.877 | 0.941 |
| 6 |  Valtteri Bottas |  | Alfa Romeo | 30 | 1'32.951 | 1.015 |
| 7 |  Sergio Perez |  | Red Bull | 20 | 1'32.958 | 1.022 |
| 8 |  Mick Schumacher |  | Haas | 24 | 1'33.085 | 1.149 |
| 9 | Lewis Hamilton |  | Mercedes | 23 | 1'33.144 | 1.208 |
| 10 |  Kevin Magnussen |  | Haas | 23 | 1'33.183 | 1.247 |
| 11 | Lando Norris |  | McLaren | 27 | 1'33.280 | 1.344 |
| 12 |  Esteban Ocon |  | Alpine | 25 | 1'33.360 | 1.424 |
| 13 | Pierre Gasly |  | AlphaTauri | 24 | 1'33.621 | 1.685 |
| 14 |  Yuki Tsunoda |  | AlphaTauri | 26 | 1'33.789 | 1.853 |
| 15 |  Guanyu Zhou |  | Alfa Romeo | 27 | 1'33.953 | 2.017 |
| 16 |  Lance Stroll |  | Aston Martin | 25 | 1'33.958 | 2.022 |
| 17 | Nico Hulkenberg |  | Aston Martin | 28 | 1'34.061 | 2.125 |
| 18 |  Daniel Ricciardo |  | McLaren | 12 | 1'34.166 | 2.230 |
| 19 | Nicholas Latifi |  | Williams | 28 | 1'34.486 | 2.550 |
| 20 |  Alex Albon |  | Williams | 22 | 1'34.735 | 2.799 |
| View full results | ||||||
