With times at the Bahrain International Circuit improving as teams shifted to more performance work, Leclerc clocked a 1m31.024s on Pirelli's C5 tyres to lead Mercedes' George Russell by four tenths.
Following two flawless days Alfa Romeo hit trouble in Sakhir, Valtteri Bottas causing a red flag as he ground to a halt with suspected gearbox problems.
It was the second red flag of the session after Red Bull's Perez lost a sensor in the opening minutes of the session.
The other notable on-track incident was a spin for Oscar Piastri in the McLaren, the Australian rookie losing control in Turn 10.
Piastri then spent a lengthy spell in the garage as McLaren was forced to strengthen the MCL60's wheelbrows.
After various drivers logged early laps in the 1m33 range on the medium C3 tyres, times took a tumble when Russell went top with a 1m31.707s on the softer C4 compound. The Mercedes driver improved upon his benchmark on the even softer C5s with a 1m31.564s and finally a 1m31.442s, while Leclerc closed the gap in second.
Leclerc then leapfrogged Russell with a double salvo of 1m31.164s and 1m31.024s on C4s, which came some 90 minutes into the session.
Russell remained second on what appeared to be a more positive morning for Mercedes, after the Brackley squad burned midnight oil investigating Friday's lack of grip. On day two Russell was also hindered by a hydraulic pump failure but on Saturday morning he was one of several drivers to move on to long runs.
Aston Martin's Felipe Drugovich was third on C5s, a full second behind Leclerc. With regular driver Lance Stroll's participation in next week's Bahrain Grand Prix still in doubt, the Brazilian reserve driver logged crucial mileage on his second half-day session before Fernando Alonso takes over in the afternoon.
Sergio Perez was the fastest of the medium runners with a 1m32.612s on C3s, followed by Alpine's Pierre Gasly and Williams driver Alex Albon.
Nico Hulkenberg was back in the Haas and took seventh, while Piastri was eighth on another tricky morning for McLaren.
Despite stopping on track Bottas still enjoyed a highly productive morning of long runs which kept him in ninth, ahead of AlphaTauri's Nyck De Vries who also stuck to race stint simulations as he logged a mammoth 87 laps.
The final afternoon of testing ahead of next week's curtain raising Bahrain Grand Prix commences at 15:15 local time.
2023 F1 Bahrain pre-season test times - Saturday morning session
| Pos | Driver | Car | Time | Laps |
| 1 | Charles Leclerc | Ferrari SF-23 | 1m31.024s | 67 |
| 2 | George Russell | Mercedes F1 W14 E Performance | 1m31.442s | 83 |
| 3 | Felipe Drugovich | Aston Martin AMR23 | 1m32.075s | 77 |
| 4 | Sergio Pérez | Red Bull RB19 | 1m32.459s | 69 |
| 5 | Pierre Gasly | Alpine A523 | 1m32.762s | 56 |
| 6 | Alexander Albon | Williams FW45 | 1m32.793s | 53 |
| 7 | Nico Hülkenberg | Haas VF-23 | 1m33.329s | 77 |
| 8 | Oscar Piastri | McLaren MCL60 | 1m33.655s | 44 |
| 9 | Valtteri Bottas | Alfa Romeo C43 | 1m36.854s | 72 |
| 10 | Nyck de Vries | AlphaTauri AT04 | 1m38.244s | 87 |
