The Triple Eight Supercars driver inherited the lead after a flurry of late pitstops in what proved to be an eventful final hour.
The six hour race at the French circuit seemed to be heading towards the Bentley squad of Andy Soucek, Wolfgang Reip and Maxime Soulet before a fire broke out during its pitstop.
The trio came into the pits under a full course yellow due to debris on the circuit.
As a result of the fire, the M-Sport car lost a full lap in the pits handing the advantage to the Garage 59 McLaren of Van Gisbergen, Rob Bell and Come Ledogar.
Van Gisbergen had the honour of bringing the McLaren 650S home for the team's second win of the season after their triumph at Monza in April.
The Kiwi took the flag 3.4s ahead of the AF Corse Ferrari 488 GT3 of Pasin Lathouras, Michele Rugolo and Alessandro Pier Guidi, which produced a spirited challenge in the final minutes.
“Making the final pitstop under the Full Course Yellow was a brilliant call and gave us the big jump we needed,” said Van Gisbergen.
“We did not have the speed of Ferrari or Bentley today but strategy and great pitstops won us the race.
“We were always on the limit of doing the shortest stop we could, so it was an impressive performance from the team. It is pretty cool to get another win.”
Rodrigo Baptista, Jan Magnussen and Filipe Albuquerque claimed the final place on the podium in the #3 Team WRT Audi R8.
Meanwhile, Soucek managed to salvage fourth for the Bentley squad despite its dramas, ahead of the Nissan GT-R GT3 of Lucas Ordonez, Mitsunori Takaboshi and Alex Buncombe.
Australia's Liam Talbot emerged victorious in the Amateur Cup class finishing 22nd outright in the #888 Kessel Racing Ferrari 458 GT3 he shared with Marco Zanuttini and Vadim Gitlin.
“Marco and Vadim did an excellent job during their stints and we had some great pitstops too,” said Talbot.
“Once I saw that our lead was big enough I controlled the race until the chequered flag.”
Countryman Matt Simmons was classified 14th in the Pro/Am class in the sister factory Nissan GT-R GT3 having completed 147 laps.
The Australian was hit by another car early in the race which forced him to pit for lengthy repairs.
Van Gisbergen and the Garage 59 squad top the Blancpain Endurance Series standings heading into next month's Spa 24 Hours from July 28-31.