The lockout by the three diesel hybrid factory cars was Audi's first since 2002 at the Sarthe circuit.
Duval's best time of three minutes 22.349 seconds was set in Wednesday night's first session with changeable weather and red flag interruptions thwarting others' efforts to go faster on Thursday.
The number one Audi R18 e-tron shared by Andre Lotterer, Marcel Fassler and Benoit Treluyer - winners for the last two years - will start in second place with the number three car of Oliver Jarvis, Lucas Di Grassi and Marc Gene in third.
Toyota, Audi's main rivals for victory on the 90th anniversary of the endurance classic, which is in its 81st edition, qualified fourth and fifth but threaten to be stronger in the race.
Kristensen is chasing his ninth Le Mans win while McNish is a double winner.
Audi, who also started on pole last year, have won the race for the last three years and 10 times in the last 13. The start is on Saturday.
Pole positions per class:
LMP1 (1st overall):
Loïc Duval - Tom Kristensen - Allan McNish (Audi R18 e-tron quattro #2, Audi Sport Team Joest) 3’22’’349
LMP2 (9th overall):
Alex Brundle - David Heinemeier Hansson - Olivier Pla (Morgan-Nissan #24, OAK Racing) 3’38’’621
LMGTE Pro (29th overall):
Robert Bell - Frédéric Makowiecki - Bruno Senna (Aston Martin Vantage GTE #99, Aston Martin Racing) 3’53’’034
LMGTE Am (38th overall):
Christoffer Nygaard - Kristian Poulsen-Allan Simonsen (Aston Martin Vantage GTE #95, Aston Martin Racing) 3’57’’776