The Japanese, sharing the number seven TS050 hybrid vehicle with Britain's Mike Conway and Frenchman Stephane Sarrazin, went round the Circuit de la Sarthe in three minutes 14.791 seconds during the day's second session.
With six minutes to go, the Toyota auto which was leading the race lost power, and completed the last lap in nearly 12 minutes - well over the six minute allowed time.
The #8 Toyota failed to turn a timed lap in second qualifying, Sebastien Buemi forced to crawl back to the pits after stopping early in the session with an oil supply issue.
Kamui Kobayashi took a huge step towards clinching Toyota pole position for the 24 Hours of Le Mans by smashing the lap record at the Circuit de la Sarthe in the second stage of qualifying on Thursday evening.
The likelihood of a direct involvement is believed to have accelerated in recent months, ever since it was confirmed that Formula E would stick to its plan to switch to one-car races in season five.
Piloting the TS050 LMP1 hybrid, Kobayashi lapped the iconic French track, made up of part permanent racing circuit and part closed public roads, in a staggering 3:14.791 - slashing two seconds from the previous record set by Neel Jani in 2015.
"I got in the vehicle with 100% confidence and when you are confident, you are quick". Kamui Kobayashi - a man famed for his ability to go absolutely nuts in a racing vehicle - has put his #7 Toyota on pole for this year's race.
"It was an incredible lap, the auto was awesome, and we went after it without any trouble whatsoever with traffic". This live blog will update continuously throughout the race, so if you can't watch all 24 hours in one sitting, check back in here to see what you've missed. Its #5 TS050 Hybrid racecar lost power under acceleration allowing the no. 2 Porsche 919 to overtake the stricken Toyota on what ended up as the last lap of the race. Meanwhile, auto No. 2 finished eight tenths of a second down on Jani in the Porsche 919 Hybrid. "But it was painful, sad and hard to forget", said Nakajima who will hope to end Toyota's 30-year wait for victory in the 85th running of the race.