Tom Kristensen, Allan McNish and Loic Duval of Audi No. 2 finished one lap ahead of Toyota No. 8 driven by Anthony Davidson, Sebastien Buemi and Stephane Sarrazin.
"This one is for Allan Simonsen," a tearful Kristensen said after taking the checkered flag. "A fantastic driver. This is for him."
The 34-year-old Simonsen was taken to the hospital after his Aston Martin spun out at high speed Saturday only 10 minutes into the race. He skidded into the barrier at the Tertre Rouge corner, where cars typically reach speeds of up to 105 mph. Simonsen died at the hospital soon after arrival, organizers said.
"Obviously, this horrible incident dampens the joy about another great Le Mans victory for Audi," Ullrich said on the team's website. "We were all completely shocked by the news of Allan Simonsen's death. This is the first fatal accident we've had to witness in 15 Le Mans years. I hope it'll remain the last."
After Simonsen's accident, Aston Martin Racing stayed in the race at the request of his family.
Sebastien Enjolras lost his life during pre-qualifying at Le Mans in 1997. The last driver fatality during the race itself was Jo Gartner in 1986. The worst crash in Le Mans history occurred when Pierre Levegh's Mercedes flew into the crowd in 1955, killing more than 80 spectators.
This was Duval's first victory at Le Mans but the third for McNish and the ninth for Kristensen, who extended his record for most titles by a driver.
Audi earned its 12th title at Le Mans, four shy of Porsche's record. The winning trio completed 348 laps in 24 hours on the 8.5-mile Circuit de la Sarthe.
"It was a complicated race," Duval said. "It's a reminder that it's a dangerous sport, even though we don't often think about it. It was very emotional. Tom lost his father in March and now he's losing a friend. That's rough."
Fifty-six cars started in the 81st edition of Le Mans, but 13 failed to finish and one car didn't complete a sufficient number of laps to be classified. In the 12th hour, but Canadian driver Tony Burgess managed to walk away from a crash.
"The conditions were very tough," said Wolfgang Ullrich, head of Audi Motorsport. "We had to make the right decisions at the right time."
At the wheel of Audi No. 3, Oliver Jarvis, Marc Gene and Lucas Di Grassi took third place, one lap off the pace.
Although Audi was much quicker than its Japanese rival, Toyota hoped fuel consumption and tire management could be decisive. But the strategy was thwarted by the changing weather and numerous safety car periods. The safety car came out 11 times, holding up the race for more than five hours.
Toyota now has four runner-up finishes at Le Mans but has never won. The only Japanese manufacturer to win was Mazda in 1991. Audi had the top three spots on the grid while Toyota started from fourth and fifth.
Toyota briefly hit the front when the Audis pitted in the second hour. But the German manufacturer started dominating the race, regaining the top three spots in the third hour under pouring rain.
However, speed is no guarantee of victory. Reliability matters just as much in a competition won by the team that completes the most laps in 24 hours, with up to three drivers alternating.
Just when Audi looked irresistible on a track that was drying out, two of its cars faced reliability issues in the seventh hour.
Benoit Treluyer's Audi No. 1 was stuck in the garage for more than 40 minutes because of technical trouble to fall out of contention, finishing fifth. The Audi No. 3 driven by Jarvis had a puncture and later had his front bodywork changed. Jarvis' Audi No. 3 overtook Nicolas Lapierre's Toyota No. 7 in the 22nd hour to make the podium.
In the next-to-last hour, Lapierre made a mistake, skidding off the slippery track at the Porsche curves to crash into the tire barrier. But Lapierre limped back into the garage and finished fourth.
In the 12th hour, Burgess' HVM Status GP No. 30 shattered into pieces in a crash.
"It was obviously a great relief when we saw him walk away from the accident," HVM Status GP technical director Rob Arnott said. "Many of the components are completely destroyed but the safety cell and everything else stood up to the impact incredibly well and it all absorbed the impact."
Martin Plowman, Ricardo Gonzalez and Bertrand Baguette finished seventh overall in Morgan-Nissan No. 35 but topped the LMP2 class.
Marc Lieb, Richard Lietz and Romain Dumas won the GTE-Pro class in Porsche No. 92, while Raymond Narac, Christophe Bourret and Jean-Karl Vernay finished first in the GTE-Am category at the wheel of Porsche No. 76.
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