The No. 8 Toyota TS050 Hybrid has been given a 60-second stop-and-hold penalty, dropping it to two minutes behind the sister Toyota Gazoo Racing entry shortly after midnight.
Sebastien Buemi served the penalty which was for speeding in a Slow Zone, separating the pair of Toyotas which are still running 1-2 but had been within several seconds of each other.
Mike Conway currently leads the race with a little over nine-and-a-half hours of the race completed.
Speculation that the No. 8 Toyota could be penalized for reversing in the pit lane has been unfounded with video evidence showing that it had been pushed by the mechanics, which is allowed per the regulations.
Rebellion Racing runs third and fourth overall with its pair of Rebellion R13 Gibsons, currently four and five laps off the lead.
G-Drive Racing is still out front in LMP2 with Andrea Pizzitola circulating fifth overall and seven laps off the Toyotas.
The car was put under investigation earlier for a pit stop infringement but has not received a penalty.
Kevin Estre heads the GTE-Pro field for Porsche while Ford Chip Ganassi Racing has moved into second with its No. 68 car driven by Sebastien Bourdais.
The front-running No. 81 BMW M8 GTE has gone into the garage with a damper issue while the No. 93 Porsche 911 RSR had an alternator change and dropped to the back of the class.
Julien Andlauer has kept Dempsey-Proton Racing in the GTE-Am lead with an almost one-minute lead over the JMW Motorsport Ferrari 488 GTE.