The #7 Toyota of Jose Maria Lopez, Kamui Kobayashi and Mike Conway has topped the second qualifying session with a time of 03:15:497.
That time was enough to hold off title rivals Sebastien Buemi, Kazuki Nakajima and Fernando Alonso, who were about half a second back with 03:15:908.
Le Mans debutant Stoffel Vandoorne was a second back with a time of 03:16:953 in third, ahead of Rebellion's Bruno Senna and team-mate Egor Orudzhev.
The LMP1 timing sheet was completed by Rebellion's Thomas Laurent, Dragonspeed's Ben Hanley and ByKolles' Tom Dillmann.
In LMP2, Dragonspeed remained on top, with Pastor Maldonado's 03:26:490 was still the quickest time, ahead of the #38 Jackie Chan DC Racing, Signatech Alpine's Nicolas Lapierre and TDS Racing's Francois Perrodo. Racing Team Nederland's Giedo van der Garde was fifth.
A late flurry of action in GTE Pro saw five cars set laps under the 3:50 mark. Defending race winner Michael Christensen went quickest with 03:39:388, ahead of Antonio Garcia in the #63 Corvette. Harry Tincknell, who was quickest yesterday, dropped to third. The top five was rounded out by the Porsches of Patrick Pilet and Gianmaria Bruni.
The #88 Dempsey-Proton Porsche of Matteo Cairoli tops the sheets in GTE Am with a time of 03:52:454, ahead of WEC championship leader Jörg Bergmeister in the Team Project 1 Porsche, with Spirit of Race's Giancarlo Fisichella third.
The third qualifying session at Le Mans kicks off at 10.00 pm local time.
