Duval was nearly three seconds faster than former Formula One driver Lucas di Grassi in the #3 Audi and within a second of last year's LMP1 pole time on the Circuit de la Sarthe.
He said the quick lap was a result of running a qualifying simulation at the end of the eight-hour session, which was affected by rain.
"It is always good to be able to finish the day at the top of the timesheets," he said. "We were trying to do a qualifying lap to see what the car was capable of.
"We didn't put a lot of fuel in and I got a clear lap. I was flat out and did a really good lap."
He added of the shunt in the #2 Audi R18 e-tron quattro: "Something hit the screen and I instinctively looked to the left.
"I got two wheels on the damp, and that's why I lost the car. It was still my fault, but it was not like I was pushing too hard."
Duval will race the car with team-mates Allan McNish and Tom Kristensen in the world-famous endurance race.
In the #1 Audi, Andre Lotterer was three-tenths off Di Grassi in third.
The Le Mans 24 Hours is on June 22-23.