Leclerc set his best lap time in the first half of the session, before the rain hit the circuit for the second time on Friday.
The rain did not prevent cars from running however, as the teams scrambled to try and get some meaningful running under their belts. Cars were running on the medium and hard tyres for the majority of the session, with drivers still struggling to successfully negotiate the first chicane.
Hamilton was second, with his Mercedes team using both drivers to test the slipstream effect in preparation for qualifying on Saturday. They will be looking for the biggest tow that they can get as straight line speed is so important at Monza, especially due to the Ferrari engine being so strong.
The other Ferrari of Sebastian Vettel finished in third, 0.201s behind his teammate. The German was closely followed by Valtteri Bottas in fourth, with the Finn topping the speed trap at 340kph. This translates to 211mph, with greater speeds expected when the car is run in qualifying trim.
Next up was the two Red Bulls, with both drivers running a very thin rear wing in order to maximise their straight line speed. Max Verstappen was only 0.003s behind Bottas, with Alexander Albon a further three tenths behind.
Toro Rosso continued their encouraging start to the weekend, with Pierre Gasly just over a second behind Leclerc's best effort.
Romain Grosjean was eighth, closely followed by the Renault of Daniel Ricciardo. Ricciardo was testing the track limits throughout the session, with the Australian kicking up some gravel at turn three.
Daniil Kvyat rounds out the top ten, with the Russian focusing on long runs and ending the session on the hard compound tyre.
It was a troubled session for Lando Norris in the McLaren, with the rookie spending the majority of the session in the garage with an oil leak. The team only managed to get him out on track to do a few timed laps at the end of the session, good enough for eighteenth.
Bahrain International Circuit - Winter testing