After nine hours at the Circuit de la Sarthe, the number seven Toyota was 7.284 seconds clear of the eight car with the number 17 SMP Racing BR Engineering car in third place but two laps down.
Britain's Mike Conway, Japan's Kamui Kobayashi and Argentine Jose Maria Lopez are sharing the seven car and chasing their first Le Mans overall win.
"Just trying to make everything clean, not to do anything silly," Conway had said after completing the opening stint and handing over to Kobayashi with the eight car more than a minute behind.
"I thought the sister car would be a little bit closer. It looks like they're struggling a little bit," he observed.
The eight car crewed by last year's winners double Formula One champion Fernando Alonso, Japan's Kazuki Nakajima and Switzerland's Sebastien Buemi closed the gap after safety car periods and mistakes by Lopez with eight hours gone.
"It’s difficult to match the other car on pure pace but we will push," commented Alonso.
The safety car was deployed in the sixth hour after a collision between Marcel Fassler's Corvette and a GTE Am Porsche driven by Japanese Satoshi Hoshino that led to the retirement of both.
The number eight went ahead in the seventh hour after another safety car period before Lopez passed Nakajima to regain the lead. The Argentine then went into the gravel at Mulsanne to drop back to second.
Alonso, Nakajima and Buemi are leading the world endurance championship and do not need to win the race to take the title.
Toyota are the only major manufacturer in the top LMP1 category and the championship battle, in a super-season that includes two editions of Le Mans, is a private one between their drivers.
Whatever happens, Sunday is guaranteed to see a Japanese driver win a major FIA-sanctioned world championship for the first time.
Alonso, who left Formula One at the end of 2018, can also become the first F1 champion to win more than once at Le Mans.
The Japanese car giant has already clinched the manufacturers' championship and is sure to take the double with the number eight car out of reach of all but their team mates in car seven.
The ceremonial starting flag for the 87th edition of the race, with 61 cars taking part, was waved by Princess Charlene of Monaco.
(Reporting by Alan Baldwin in London, editing by Clare Fallon)
