Lotterer cut through the night in a best time of 3:25.45s to end the first of two qualifying sessions 1.1s quicker than Tom Kirstensen in the #2 e-tron.
The Dane had joined his team-mate in making a late run for the top spot by fell short after finding traffic.
Loic Duval put the #3 Audi Ultra in third position, while the #7 Toyota (Wurz/Lapierre/Nakajima)and #4 Audi Ultra (Rockenfeller/Jarvis/Bonanomi) rounded out the top five.
The #8 Toyota (Davidson/Buemi/Sarrazin) was sixth despite completing just five laps in the earlier practice session before requiring an engine change.
The #21 Strakka HPD (Leventis/Watts/Kane) was the fastest of the non-factory LMP1 entries, while the #46 TDS Oreca-Nissan (Beche/Thiriet/Tinseau), #97 Aston Martin (Fernandez/Mucke/Turner) and #79 Flying Lizard Porsche (Neiman/Pilet/Pumpelly) led the way in LMP2, GTE Pro and GTE Am respectively.
The two Australian drivers enjoyed solid starts to race week, with David Brabham's #22 JRM HPD and John Martin's #25 ADR ORECA-Nissan 10th and ninth in LMP1 and LMP2 respectively.
The Nissan DeltaWing lapped 26th fastest despite losing tack time when a jolt from the circuit's kerbing tripped the car's masterswitch and onboard fire extinguisher.
A second qualifying session tomorrow will combine with the opening night of running to set the grid for the weekend's race.