The Monegasque lapped the 5.4-kilometer long Sakhir desert track in one minute 29.569 seconds, 0.169 seconds clear of team mate Sebastian Vettel.
The Ferrari pair have finished one-two at the top of the timesheets in every session this weekend.
Reigning world champion Lewis Hamilton was third for Mercedes, waiting until the dying seconds to put in his flying lap.
The Briton edged team mate Valtteri Bottas, who won the season-opener in Australia two weeks ago, by less than a tenth of a second.
But he was still a 0.765 seconds off Leclerc's pace.
Tipped as the pre-season favourites after posting strong times in testing, Ferrari went into the weekend hopeful their mysterious lack of pace at Melbourne's Albert Park track was merely a one-off.
Historically strong in Bahrain, with a record six wins including two in a row for Vettel in the last two years, they have dominated every session so far.
The closest that Mercedes have managed to get to them has been 0.6 seconds.
The margin is misleading, however, Ferrari cautioned after Friday's practice sessions while Mercedes boss Toto Wolff said the red cars had only a "tiny edge" on his team's challengers.
With the battle for pole position set to take place in cooler conditions in the evening under the floodlights, unlike the hot and sunny conditions drivers faced in the final practice session, the gaps could well close up.
Behind the top-four, Romain Grosjean of Haas led a close midfield group in fifth.
Nico Hulkenberg was sixth for Renault ahead of McLaren's Lando Norris.
Max Verstappen was the quickest Red Bull in eighth ahead of Carlos Sainz's McLaren and Daniil Kvyat who rounded out the top-ten.
Fallen champions Williams continued to prop up the timesheets. British rookie George Russell was ahead of Pole Robert Kubica with both drivers nearly four seconds off the pace.
(Editing by Christian Radnedge)
