However, it still managed to finish third and fourth, with Hamilton leading Bottas for the first time this weekend - however he was just under four-tenths down on Leclerc.
Max Verstappen was fifth for Red Bull, but tapped the wall towards the end of the session at Turn 13 after spinning.
As has been the case for much of the season, the midfield pack is set to see an extremely close fight during the qualifying session later this afternoon.
There was more trouble for Daniil Kvyat as he was forced to park up his Toro Rosso at the side of the circuit, as he did yesterday.
Honda confirmed that the issue was related to the engine, and that the Russian driver will not compete in his home qualifying event later his afternoon.
The Mexican had two major lock-ups at Turn 13 on two different sets of tyres, destroying both in the process.
Bahrain International Circuit - Winter testing