Frenchman Eric Duval, who had gone quickest in practice earlier on, put the #2 R18 e-tron quattro on top.
Loic Duval snatched provisional pole position for the Le Mans 24 Hours in an opening qualifying session that was brought to a premature end by barrier damage at the second Mulsanne chicane.
Frenchman Duval, who hadgone quickest in practiceearlier on, put the #2 R18 e-tron quattro on top initially before improving to a 3m22.349s time that would go unbeaten for the rest of the session.
That fact was helped by the final 55 minutes of running being cancelled due to barrier damage incurred when expected LMP2 front-runner Pierre Thiriet lost control of the #46 TDS ORECA-Nissan at the second Mulsanne chicane.
Thiriet was unhurt, but after a 40-minute red-flag period, race officials deemed the barriers were not able to be repaired to a satisfactory standard and declared the session 15 minutes before time.
With no late improvements possible, Audi ended the day with successive one-two-three results.
Toyota had temporarily broken the German marque's dominance, with the #7 TS030 HYBRID of Alex Wurz/Nicolas Lapierre/Kazuki Nakajima running second early on.
It dropped down the order as first Marc Gene and then Andre Lotterer improved in the #3 and #1 Audis to end the session second and third. The Toyota was fourth - 4s down on Duval - when the red flags flew.
There was worse news for the sister #8 Toyota, which managed just 10 laps - enough to put it sixth overall - before Sebastien Buemi was forced to pull to a halt at Arnage due to a loss of power.
The car was later recovered to parc ferme, but not before the session was effectively ended by Thiriet's crash.
In LMP2, British IndyCar convert Mike Conway earned his G-Drive/Delta-ADR squad the top spot with an early 3m39.535s.
That proved more than a second faster than anyone else could manage. Franck Mailleux, Conway's nearest challenger in the #43 Morand Morgan-Judd, was second fastest but more than 1.2s adrift.
Karun Chandhok's Murphy Prototype squad qualified ninth in the LMP2 category, and 17th overall.
It was a much tighter affair in GTE Pro, with less than a second to choose between the top seven cars.
The Prodrive-run factory Aston Martin team eventually ended top of the pile courtesy of Frederic Makowiecki in the #99 Vantage, narrowly ahead of the #51 AF Corse Ferrari 458 of Gianmaria Bruni/Matteo Malucelli/Giancarlo Fisichella.
The #97 and #98 Vantages, raced by Peter Dumbreck/Stefan Mucke/Darren Turner and Bill Auberlen/Paul Dalla Lana/Pedro Lamy, were third and fourth fastest respectively.
Aston Martin also ended on top in GTE Am, with Christoffer Nygaard/Kristian Poulsen/Allan Simonsen narrowly edging out the lead #88 Proton Porsche 911. Simonsen was at the wheel when the car's best time was set.
Four cars failed to set a time. The #41 Greaves Motorsport Zytek Nissan plus the #66 JMW and #57 Krohns Ferrari all suffered heavy damage in practice crashes while, fresh fromwinning a court caseagains its aggrieved car designer, the Lotus squad did not get its #32 LMP2-spec T128 out either.