Alonso's victory completes the second part of motorsport's "triple crown" for the two-time Formula 1 world champion.
The McLaren driver, who will remain in France for next weekend's Grand Prix at Le Castellet, has yet to win the Indianapolis 500 - a race he led a year ago before an engine failure - to match the late Graham Hill's achievement.
But the magnitude of Sunday's win was every bit as big for Alonso's team mates. We were close to winning, but missed the opportunity.
Late at night, after Buemi drew a one minute "stop and go" penalty, Alonso took over and sparkled in the darkness as he closed the gap. "I was in the zone and I pushed to catch up", he said.
The started the race from pole position and never looked back, going on to dominate the race with a 1-2 finish.
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.
It was Toyota's first victory at the 20th attempt, and the first win for a Japanese manufacturer since Mazda's success in 1991.
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Nakajimi and Buemi saw the race out in a historic win not only for Alonso or Toyota, but also for Japan.
Their work on reliability over the winter has paid off with no sign of the mechanical failures that had plagued the team since 2012.
Toyota made history this past weekend when it clinched a maiden victory at the 24 Hours of Le Mans.
Instead, he handed over to Nakajima, who then passed fellow-Japanese Kamui Kobayashi in the #7 Toyota for the lead.
Alonso's auto was left more than two minutes behind the other Toyota but the Spaniard managed to claw back the difference through the night, putting Nakajima in position to retake the lead from Kobayashi early on Sunday.
Although the final rankings may make it look like an easy win, with some substantial leads, it wasn't the case as Toyota's number eight was involved in an early crash with a Rebellion auto.
Jenson Button's Le Mans debut was hard, his SMP Racing BR1 losing two hours with a technical problem early on.