The Fuoco’s No51 Ferrari team-mate Alessandro Pier Guidi set a time 0.9sec slower than the lead Ferrari, with Brendon Hartley’s No8 Toyota lining up third.
The Kiwi’s Japanese team-mate Kamui Kobayashi had his fastest lap deleted, meaning he’ll start fifth, with the No75 Porsche Penske of Felipe Nasr fourth-quickest.
Earl Bamber put the No2 Cadillac sixth, while his No3 Ganassi team-mate Sébastien Bourdais saw his chances go up in smoke – literally – when his his machine caught fire, forcing him to stop at the first chicane.
The two Cadillacs sandwiched the No5 Porsche Penske of Frederic Makowiecki who will begin the race seventh.
Paul Loup Chatin took a brilliant LMP2 pole for IDEC Sport, seeing off the pre-session favourite of Jota Sport’s Pietro Fittipaldi, while Ben Keating put his Chevrolet Corvette first in GTE-Am.