Japanese driver Kazuki Nakajima set the fastest lap, a three minute 15.377 effort that was close to the record of 3:14.791 set last year by compatriot Kamui Kobayashi, who is in the number seven car.
Nakajima, who shares the hybrid with Alonso and Switzerland's Sebastien Buemi, had already set the provisional pole on Wednesday but improved on that time to beat the sister car by almost two seconds.
"The lap was great, the car setup was almost perfect for me and I had no traffic, which was very lucky," said Nakajima, who was pushing hard for the record. "Let's hope everything goes well in the race."
Double Formula One world champion Alonso is competing for Toyota in the full World Endurance series this season as well as carrying out his grand prix duties with McLaren and is the centre of attention at Le Mans.
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The Spaniard packed in plenty of night driving experience towards the end of the session with light rain falling and the track emptying of traffic.
The 86th running of the race at the Sarthe circuit starts on Saturday at 1300 GMT (1500 local).
Toyota are clear favourites for victory as the only major manufacturer entered in the top LMP1 category after champions Porsche quit but can take nothing for granted after losing out in 2017 due to unreliability.
This year's race will be their 20th attempt to become only the second Japanese marque after Mazda to triumph in the endurance classic.
The big question is, assuming they run untroubled throughout, which of the two factory crews will end up as winners.
For Alonso, the aim is to tick off the second part of the 'Triple Crown of Motorsport', leaving only the Indianapolis 500 to conquer. He has also won the Monaco Grand Prix twice.
Only one man has completed the Triple Crown -- the late British world champion Graham Hill.
Jenson Button, the 2009 Formula One world champion, will start seventh for the Russian-backed SMP Racing team's number 11 car.
Colombian Juan Pablo Montoya, already a Monaco Grand Prix winner and Indianapolis 500 champion, will start 24th in the United Autosports entry that is competing in the lower LMP2 category.
(Reporting by Alan Baldwin in London, editing by Peter Rutherford)
