Alonso, a double Monaco Grand Prix victor and twice F1 world champion, is aiming for the "Triple Crown of Motorsport", and the Indianapolis 500 is now the only box remaining to be ticked.
The 36-year old Spaniard and team-mates Kazuki Nakajima and Sebastien Buemi secured a two-lap victory.
The trio put the #8 vehicle on pole, ahead of team mates Kamui Kobayashi, Mike Conway and Jose Maria Lopez, with their nearest challenger a staggering four seconds further back in third.
Twice a Monaco Grand Prix victor, he now wants to win the Indianapolis 500.
The last F1 driver to win at Le Mans was Germany's Nico Hulkenberg with Porsche in 2015, but he only entered one race, while Alonso signed for the entire endurance season and, after winning the first two rounds, is leading the overall standings.
"Le Mans once a year is not enough!"
Alonso will now turn his attention back to F1 with the championship returning to France for the first time in a decade with a race at Paul Ricard. The rules are targeting a 3:20.00 lap around Circuit De La Sarthe, just six seconds slower than the current lap record, set by Kamui Kobayashi in 2017.
His auto was out of contention early on after spending two hours in the pits with an engine problem. Jenson Button's BR Engineering BR1, which included Vitaly Petrov and Mikhail Aleshin, was pulled from the race in the final hour. However, as time has shown, having the fastest auto is no guarantee of success.
Hayden reckons that the team's 12-lap deficit to Toyota was at least partially down to these mechanical and reliability problems rather than the regulations. "It has been our dream to win Le Mans and finally we have achieved it", he said. Last year, unreliability - despite prodigious pace - meant the team didn't score a win either.
The triumph, expected after champions Porsche withdrew past year, came at the 20th attempt for Toyota who became only the second Japanese manufacturer to win the world's greatest endurance race after Mazda in 1991.
But Toyota insisted that the two cars went into the race with equal chances of winning.
Nakajimi and Buemi saw the race out in a historic win not only for Alonso or Toyota, but also for Japan.
These questions will be hanging over him when he returns to his F1 role with McLaren at next weekend's French Grand Prix.