Emanuele Pirro, Frank Biela and Marco Werner made history by becoming the first drivers to win the Le Mans 24-hour race in a diesel-powered car.
Audi have won six of the last seven races at Le Mans
The Audi R10 Diesel completed a record 380 laps of the La Sarthe circuit, with Pirro at the wheel for the finish.
French trio Sebastien Loeb, Eric Helary and Franck Montagny took second in the No 17 Pescarolo-Judd, four laps adrift.
Scotsman Allan McNish was third in the other Audi, which came in 13 laps down after suffering mechanical problems.
It marked the end of a six-year unbeaten run in the event for McNish's team-mate Tom Kristensen of Denmark.
McNish, Kristensen and Rinaldo Capello had started the race on pole.
But their car was hit by a problem with the windscreen, and more serious trouble saw it return to the pits for lengthy work and slip down to 16th at one stage.
"It's a double-edged sword - from a team point of view it's a fantastic achievement but we are driven to win," said McNish.
I wanted to be a part of this project so badly when I was told about the adventure
"We knew we had the competitiveness to do it."
After losing the lead briefly on the 14th lap, Werner, Biela and Pirro held on to it throughout the race.
The only delay to affect their progress was a gearbox change after 11 hours, but the repairs took less than 10 minutes.
Audi led every lap as the diesel cars, as expected, enjoyed greater fuel economy but also proved quicker than their petrol-powered rivals.
It is the sixth time Audi have won the race, and the fourth Le Mans victory for both Biela and Pirro.
"I wanted to be a part of this project so badly when I was told about the adventure," said Pirro.
"I couldn't even ask to win the race because that would be too much - I just wanted to be here."
The Pescarolo team had cut the deficit to two laps during the night.
But Montagny then slid into a gravel trap at Mulsanne corner and, although he managed to restart the car after it was pushed into an exit road, the lost time ended their hopes.
The second Pescarolo Sport team finished fifth after a race plagued with mechanical issues.
GT1 entrant Corvette Racing, in which Britain's Oliver Gavin partnered ex-Formula One drivers Jan Magnussen and Olivier Beretta, was fourth.
The Racing for Holland team had been on course for third until just past the midway point, when Malaysia's former F1 driver Alex Yoong crashed his Dome-Judd into the barriers after his throttle stuck open.
Aston Martin completed the top six, with Andre Piccini taking the flag for second in the GT1 class in the car he shared with Oxford-based Darren Turner and Tomas Enge.
There was British success in the LMP2 category as well, with Mike Newton and Andy Wallace teaming up with Brazilian Thomas Erdos to take the honours in their Lola.