The celebrated British marque took the honours for the first time since 1930 with the car driven by Italian Rinaldo Capello, Tom Kristensen of Denmark and Briton Guy Smith.
It was a memorable day for the distinctive British racing green-liveried team as their other car driven by Aussie David Brabham and British duo Mark Blundell and Johnny Herbert, crossed the line in second.
Bentley captured five editions of the ultimate endurance test between the First and Second World Wars, but then retired only to return to the fray in 2000.
Owned by the giant Volkswagan group, they placed third in 2001 and fourth last summer and were firm favourites to regain winning ways after a hat-trick of wins for Audi.
As Capello watched his teammate Smith cross the line he said: "I can't tell you how I'm feeling this is something unique.
"I'm absolutely exhausted we pushed hard right from the start."
Capello, Kristensen and Smith set off from pole position and proceeded to lead from start to finish, coming in two laps clear of their sister car.