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. Alonso said on Sunday he remained committed to the full endurance championship with Toyota through to next June, with the current "super season" featuring two editions of Le Mans. Both cars ran reliably, with Alonso and his crew running second for much of the opening stint before the Spaniard delivered a stunning spell overnight to reduce the deficit, before Nakajima passed Kobayashi to seize a lead they would never relinquish.
The number 7 auto was always out of reach.
In the 16th hour of the race, Nakajima retook the lead and the number eight vehicle was in control for the duration.
The auto will form the base of a racer, set to compete in the just-announced "hypercar" class of the FIA World Endurance Championship when new regulations take force in 2020.
The number seven Toyota - driven by Japan's Kamui Kobayashi to the checkered flag and shared with Briton Mike Conway and Argentina's Jose Maria Lopez - crossed the line in one-two formation with Nakajima but two laps down. It finished second behind the sister auto giving Toyota a 1-2 finish. Near the end, he also missed a signal to pit for fuel, and did a slow lap largely on electric power as a result.
Fernando Alonso has always been regarded as one of the all-time great racing drivers and the best along with Lewis Hamilton in the current era of F1, but he has found success hard to come by in grands prix in recent years.
Toyota's win is just the second by a Japanese manufacturer, following Mazda's success in 1991.
It just shows the effects of downforce and diffuser pressure as cars attain blistering speeds across the track.
Before the race, Buemi who, like Nakajima, had been vainly chasing a Le Mans victory since 2012, said Alonso "was a real plus for the team".
There has been speculation that a Le Mans win could hasten the 36-year-old's departure from Formula One, with McLaren still a long way off the podium.