Estre was the last Hypercar runner to cross the chequered flag and clocked a time of 3m24.634s in the #6 factory Porsche Penske 963, overhauling a top-two lockout by Cadillac, after the #3 Cadillac that had led for the majority of the 30 minute session in the hands of Sebastien Bourdais.
Bourdais had set the initial pace in the pole shootout with a time of 3m25.294s in the additional entry fielded by Chip Ganassi at Le Mans, before staying out in the first run and improving to a 3m24.816s.
All cars were back out on track for their second run when Dries Vanthoor suffered a heavy hit to the barriers going into Indianapolis, causing the red flag and leaving the #15 BMW M Hybrid V8 that had topped the first qualifying session out of the fight for pole position.
Bourdais elected to sit out when Hyperpole resumed with just under eight minutes left on the clock, with his initial effort appearing to be enough to claim pole position for Cadillac.
An improvement for Alex Lynn in the sister #2 V-Series.R entry provisionally took pole for Cadillac in a 1-2, but Estre spoiled the party for the General Motors brand with his last-ditch effort as he narrowly claimed pole for Porsche.
The two Ganassi-run Cadillacs will now line up second and third, with the two factory Ferraris the next up in fourth and fifth. Alessandro Pier Guidi was the quicker of the two 499Ps, the #51 machine, heading the sister car qualified by Antonio Fuoco by over four tenths of a second.
The sole Alpine A424 that progressed into the final leg of qualifying took sixth with Paul-Loup Chatin, ending up just over a second off the pace of polesitter Estre.
#51 Ferrari AF Corse Ferrari 499P: Alessandro Pier Guidi, James Calado, Antonio Giovinazzi
Photo by: Alexander Trienitz
Only seven Hypercar entries took part in the pole shootout, with Jota still rebuilding its #12 Porsche 963 LMDh after Callum Ilott damaged the original chassis in night practice on Wednesday.
The first of the two Jota Porsches is set to line up seventh on the grid, with the #15 BMW that Vanthoor crashed ending up eighth.
In LMP2, Louis Deletraz claimed pole position with a brilliant effort of 3m33.217s in the #14 AO by TF ORECA-Gibson 07 that is entered in the Pro-Am subclass.
That put him six tenths clear of Job van Uitert in the #28 IDEC Sport entry, with Mathias Beche taking third in the #65 Panis Racing ORECA.
Deletraz was already leading the LMP2 field when the session was halted for Vanthoor’s Hypercar crash, but the Swiss driver managed to find even more time on his final run to secure pole position in the intermediate class.
Wednesday qualifying pacesetter Malthe Jakobsen made no improvement in the final minutes, consigning the #37 Cool Racing entry to sixth among the eight runners.
#70 Inception Racing McLaren 720S LMGT3 Evo: Brendan Iribe, Ollie Millroy, Frederik Schandorff
Photo by: Marc Fleury
Meanwhile, Inception Racing’s Brendon Iribe took top honours in the LMGT3 division despite wrecking a quick lap with a spin coming out of the final chicane.
Iribe managed to deliver a late improvements in the #70 McLaren 720S GT3 to qualify a massive eight tenths clear of the chasing pack led by championship leader Aliaksandr Malykhin in the #92 Manthey PureRxcing Porsche 911 GT3 R.
Giacomo Petrobelli finished just 0.010s adrift of Malykhin in third in the #66 JMW Motorsport Ferrari 296 GT3, making it two non-regular WEC cars inside the top three.