The Scot, driving the hybrid Audi R18 e-tron quattro, set a best time of 3m25.927s in the afternoon session of the eight-hour test. That was half a second quicker than Andre Lotterer in the second Audi hybrid, which recorded a 3m26.468s.
McNish, who again co-drives with Tom Kristensen and Rinaldo Capello, said: "The car was very good. We had some ideas after Spa [the hybrid's race debut] and Dindo and Tom took them further, and then I continued to improve the car."
McNish's Audi finished the session early after a crash at Tertre Rouge, which he stressed was his fault. He could have driven back to the pits, but with only one hour to go, the team decided not to risk damaging the car further.
Loic Duval was third fastest in the fastest of non-hybrid Audi turbodiesels. His R18 ultra was only a tenth slower than Lotterer on a 3m26.561s.
Alex Wurz set the best Toyota time of the test during the afternoon. He was only seven tenths behind the third-place Audi.
The fastest time set by a privateer LMP1 car was Danny Watts' morning best in the Strakka Racing HPD ARX-03a. His 3m34.243s was more than second faster than Andrea Belicchi's time in the fastest of the Rebellion Racing Lola-Toyota B12/60s.
Olivier Pla was fastest in LMP2 in both sessions aboard the OAK Racing Morgan-Nissan 2012 LMP2. The Frenchman tested this car, as well as the Judd/BMW-powered version that he will drive in the race, in the absence of Bas Leinders and Maxime Martin.
Luxury Racing Ferrari driver Frederic Makowiecki's time of 3m58.869s from the morning session stood as the best time in GTE Pro. Oliver Gavin was only just over a tenth behind in the afternoon aboard the best of the Corvette C6.Rs.
Allan Simonsen was fastest in GTE Am aboard the factory-entered Aston Martin Vantage GTE.