In the final on-track running before Hyperpole qualifying, Kamui Kobayashi recorded a best effort of 3m26.796s at the wheel of the #7 Toyota GR010 HYBRID - around half a second quicker than he managed during first qualifying on Wednesday.
Brendon Hartley backed that up with a 3m27.115s in the sister #8 car to go second-quickest ahead of the two Glickenhaus 007 LMHs.
The American boutique marque's best lap was a 3m27.466s from Olivier Pla in the #708 car, a little under seven tenths off the pace and marginally slower than his first qualifying benchmark, while Ryan Briscoe posted a 3m28.073s in the sister #709 machine.
Propping up the order in the five-car Hypercar class was Alpine's grandfathered A480-Gibson LMP1, despite receiving a power increase in a revised Balance of Performance issued as the three-hour session began.
Matthieu Vaxiviere was 2.4 seconds down on Kobayashi with a 3m29.259s, only a minor improvement on Nicolas Lapierre's effort in the #36 machine in first qualifying.
Toyota's #8 car lost time with an electrical glitch that prompted Ryo Hirakawa to briefly stop on track between Indianapolis and Arnage corners before bringing the stricken machine back for a trip to the garage.
That was prior to a 20-minute red flag period caused by a major crash for the #13 TDS Racing Oreca LMP2 of Philippe Cimadomo at Corvette Curve, the result of slight contact with the #31 WRT car of Sean Gelael.
Topping the times in the LMP2 class were United Autosports' pair of ORECA 07s, which both set their fastest times in the final five minutes of the session.
Filipe Albuquerque was quickest in the class on a 3m20.964s aboard the #22 United entry, going less than a tenth faster than Alex Lynn in the #23 car.
Robin Frijns, who set his best lap of 3m31.030s immediately after the red flag period, was demoted to third place in the #31 WRT car, ahead of Yifei Ye in the #37 Cool Racing entry and the best of the Jota machines, the #38 car of Antonio Felix da Costa.
Most of the other major incidents during the session involved LMP2 runners.
Duqueine man Reshad de Gerus suffered an early off at Indianapolis, while following the red flag period Sebastien Page crashed the Graff car at the same part of the track, with both incidents being covered off with slow zones.
Miro Konopka also had an excursion through the gravel at the Dunlop chicane in the ARC Bratislava car, although he was able to get going again.
Corvette Racing was again the team to beat in GTE Pro as Nick Tandy set a best time in class of 3m52.307s aboard the American marque's full-time WEC entry, the #64 C8.R.
A little under half a second down in second was the best of the factory Porsche 911 RSR-19s, the #91 machine of Richard Lietz, followed by the #63 Corvette of Antonio Garcia and the #92 Porsche of Michael Christensen.
Ferrari's pair of works 488 GTE Evos occupied fifth and sixth places in class, with Antonio Fuoco giving the Italian marque its best laptime aboard the #52 entry.
Mikkel Pedersen set the pace in GTE Am with a 3m54.386s aboard the #46 Team Project 1 Porsche, beating the TF Sport Aston Martin Vantage of Henrique Chaves by just over two tenths.
Hyperpole qualifying, involving the top six cars from each class, begins at 8pm local time.
