The Italian manufacturer locked out the top two spots with its pair of 499P Le Mans Hypercars, besting the two Toyota GR010 HYBRIDs that finished third and fourth.
Alessandro Pier Guidi set an impressive 3m25.412s in the #51 Ferrari with around 15 minutes to go, despite getting slightly held up late in the lap by a GTE Am Aston.
But moments later he was usurped by the sister #50 car of Antonio Fuoco, who posted a 3m25.213s to grab the top spot.
The early pace was set by the #7 Toyota of Kamui Kobayashi, who put in a 3m25.485s at the very start of the session – which ultimately left him 0.3s behind the Ferraris, and fractionally ahead of Brendon Hartley in the sister #8 car.
Next up in the two-by-two formation from the leading manufacturers were two of the Porsche 963 LMDhs, Frederic Makowiecki in the #5 heading Felipe Nasr in the #75 as both were 0.6s behind the Ferraris.
The final two cars from the Hypercar class to make it through to the eight-car Hyperpole shootout were the two Cadillac V-Series.R LMDhs – Sebastien Bourdais in the #3, just ahead of Earl Bamber in the #2 and both less than a second off the pace.
Kevin Estre’s #6 Porsche was the first car to miss out and will therefore start ninth, having missed the cut-off by almost a second.
Peugeot failed to get either of its 9X8 LMHs into the top eight, with Mikkel Jensen 10th in the #93 car ahead of Loic Duval in the #94 machine.
The Hypercar field was rounded out by the Action Express Caddy, the two Glickenhaus 007s and the Vanwall Vandervell 680, while JOTA’s privateer Porsche 963 did not set a time in the session and will therefore start last.
The hour-long session started with two early red flags, the first caused by a collision between the #22 United Autosports LMP2 machine of Filipe Albuquerque and the #36 Alpine ORECA of Matthieu Vaxiviere when they were jostling for position into the final chicane.
The session had only just been restarted when it was halted again, this time by the #37 Cool Racing LMP2 entry of Malthe Jakobsen skating into the Indianapolis barriers.
For the majority of the session, the LMP2 leaderboard was headed by the #28 JOTA entry of Pietro Fittipaldi, his 3m34.751s good enough to beat the #41 WRT-entered ORECA of Louis Deletraz by just two thousandths of a second.
The #63 Prema ORECA of Mirko Bortolotti made a late jump to third ahead of the #48 IDEC Sport and #10 Vector Sport cars.
There was late drama in the GTE Am class with the top time changing hands several times in the closing stages.
Charlie Eastwood’s TF Sport Aston Martin Vantage had topped the times for much of the hour before a flurry of late improvements.
First up, with just four minutes to go, Nicky Catsburg in the sole Corvette C8.R emerged from the pits following repairs after Nico Varrone’s Terte Rouge practice crash to shoot to the top of the times on his very first flying lap.
But he was shuffled back to an eventual third following a pair of late efforts from Ferrari drivers.
Davide Rigon in the #54 AF Corse 488 looked to have snared top spot, before he was pipped by the #83 Richard-Mille backed sister car of Alessio Rovera moments after the chequered flag went out.
Cars progressing to Hyperpole:
Hypercar
#50 Ferrari AF Corse
#51 Ferrari AF Corse
#7 Toyota Gazoo Racing
#8 Toyota Gazoo Racing
#5 Porsche Penske Motorsport
#75 Porsche Penske Motorsport
#3 Cadillac Racing
#2 Cadillac Racing
LMP2
#28 JOTA
#41 Team WRT
#63 Prema Racing
#48 IDEC Sport
#10 Vector Sport
#47 COOL Racing
#923 Racing Team Turkey
#9 Prema Racing
GTE Am
#83 Richard Mille AF Corse
#54 AF Corse
#33 Corvette Racing
#25 ORT by TF
#57 Kessel Racing
#55 GMB Motorsport
#21 AF Corse
#74 Kessel Racing