Kazuki Nakajima ended up fastest over the course of the three-hour session, posting a 3m21.656 aboard the #8 Toyota TS050 HYBRID in the dying stages.
That eclipsed Kamui Kobayashi's best time in #7 car, a 3m21.990s.
The #7 Toyota didn't record a representative time for the first hour of the session because it only completed installation laps as part of the aerodynamic calibration process for the latest Le Mans body package on the car.
The best of the Rebellion Racing privateer LMP1 entries was just over a second down on the second of the Toyotas.
Gustavo Menezes posted a 3m23.155s in the #1 Rebellion-Gibson R-13, which compared with the 3m25.216s from the team's second car shared by Romain Dumas, Louis Deletraz and Nathanael Berthon.
The ByKolles ENSO CLM-Gibson P1/01 driven by Tom Dillmann, Oliver Webb and Bruno Spengler brought up the rear of the P1 field on a 3m28.442s.
The times were slower than in first free practice for Le Mans last year. Kobayashi was fastest in the opening four-hour afternoon session on a 3m18.091s in 2019.
Danish High Class squad led the way in the LMP2 class courtesy of a 3m29.873s from Le Mans debutant Kenta Yamashita aboard its ORECA-Gibson 07.
The Toyota junior driver eclipsed a 3m29.918s from Giedo van der Garde in the TDS Racing-run Racing Team Nederland ORECA with 20 minutes remaining to make it two Michelin-tyred cars at the top of the order.
Third place went to the Goodyear-shod Jota Sport ORECA in which Antonio Felix da Costa set a 3m31.206s early in the session.
The French Duqueine team end up fourth with a 3m31.309s, while the Jota-run Jackie Chan DC Racing entry was fifth on 3m31.348s.
The two factory Aston Martins were on top in GTE Pro for the majority of the session.
Alex Lynn ended up fastest on a 3m53.930s, which was more than a second up on the 3m54.992s recorded by Nicki Thiim in the sister Vantage GTE.
James Calado was close behind on a 3m55.186s in his factory AF Corse Ferrari 488 GTE Evo.
That was eight tenths quicker than the 3m55.999s from the second of the works Ferraris shared by Davide Rigon, Miguel Molina and Sam Bird.
The two privateer GTE Pro Ferraris run by Risi Competizione and Scuderia Corsa took fifth and sixth positions. The two factory Porsche 911 RSR-19s brought up the rear of the eight-car GTE Pro field.
GTE Am was led by the works-run Aston Martin Vantage GTE on a 3m55.484s from Ross Gunn. That put the car eight tenths up on the HubAuto Ferrari in second place.
The session was briefly red flagged during its middle hour when the #89 GTE Am Project 1 Porsche had to be recovered from Indianapolis.
Practice resumes 2:00pm local time before the first qualifying session at 5:15pm. The fastest six cars in each class (or all the P1s) will go through to 30-minute Hyperpole session.