The German, four times a world champion with Red Bull and Monaco winner in 2011, lapped the metal-fenced streets with a best time of one minute 16.143 seconds in a session red-flagged after team mate Kimi Raikkonen hit the barriers.
Mercedes duo Nico Rosberg, winner of the last two Monaco races from pole position, and world champion Lewis Hamilton were close behind with qualifying to follow later.
A Ferrari has not been on pole position in Formula One since July 2012.
Rosberg was 0.218 slower than his compatriot while Hamilton, fastest in both of Thursday's sessions but unhappy with the handling of his on Saturday, was 0.562 off the pace.
Australian Daniel Ricciardo was fourth quickest for Red Bull, ahead of Spanish rookie Carlos Sainz in a Toro Rosso and Raikkonen, who crashed at Sainte Devote just after setting his best lap.
Dutch teenager Max Verstappen, who was second fastest behind Hamilton in Thursday's opening practise, was ninth on the timesheets after spinning and clouting the barriers, damaging the rear wing, at the last corner.
Hamilton leads Rosberg by 20 points in the championship after five races.
(Editing by Amlan Chakraborty)
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