Hamilton's fastest lap time was a 1:08.320, which was almost a second faster than Sebastian Vettel's session topping fine from FP2 on Friday afternoon.
Ferrari occupied the third and fourth positions, with Charles Leclerc leading his teammate Sebastian Vettel by half a tenth.
Leclerc has had a fresh engine fitted for the weekend, meaning he will take a ten-place grid penalty for the start of Sunday's grand prix.
Alexander Albon was fifth fastest in the second Red Bull, however he was eight-tenths of a second down on his teammate Verstappen - with Bottas filling out the top six.
Robert Kubica set the most lap times out of any driver during the session, as he rounded the circuit 23 times. The Pole was attempting to make up for lost time from Friday.
Kubica sat out the opening session as Nicholas Latifi drove his car, and in the afternoon session, he found himself in the wall only minutes into the session.
Bahrain International Circuit - Winter testing