Lotterer, who won the event last year with Switzerland's Marcel Faessler and France's Benoit Treluyer in the number two diesel Audi, put in a best lap of three minutes 23.787 seconds in the number one R18 e-tron car.
"I did not get all the perfect sectors together, but I think we can still be happy," said Lotterer.
Audi also took second place in qualifying for the 80th edition of the race at the high speed Sarthe track with the R18-ultra driven by French duo Romain Dumas and Loic Duval as well as Spaniard Marc Gene.
Toyota qualified third on their return to Le Mans after a 13-year absence with Britain's Anthony Davidson at the wheel of their petrol hybrid for the final quick lap in dry and warm conditions.
Denmark's eight-times Le Mans winner Tom Kristensen will be fourth on the grid in the number two Audi e-tron he shares with Britain's Allan McNish and Italian Rinaldo Capello.
Another former F1 driver, Karun Chandhok, was on course to become the first Indian to start the race after the JRM Honda qualified 11th with Australian David Brabham and Scotland's Peter Dumbreck.
The team had a difficult day, however, after damaging the gearbox on Wednesday.
"Yesterday I hit some debris through Tertre Rouge and the car felt like it took off. We didn't know until we checked thoroughly overnight but the impact of coming back to ground cracked the gearbox," said Chandhok.
"The team then decided to change the engine, which was pretty logical considering we were changing tomorrow anyway.
Although I would have liked to drive tonight, I'm just looking forward to getting behind the wheel at my first Le Mans on Saturday."
1. P1 Fassler/Lotterer/Treluyer Audi e-tron 3m23.787s
2. P1 Dumas/Duval/Gene Audi Ultra 3m24.078s
3. P1 Davidson/Buemi/Sarrazin Toyota 3m24.842s
4. P1 Capello/Kristensen/McNish Audi e-tron 3m25.433s
5. P1 Wurz/Lapierre/Nakajima Toyota 3m25.488s
6. P1 Bonanomi/Jarvis/Rockenfeller Audi Ultra 3m26.420s
7. P1 Leventis/Watts/Kane Strakka HPD 3m29.622s
8. P1 Prost/Jani/Heidfeld Rebellion Lola-Toyota 3m29.837s
9. P1 Belicchi/Primat/Bleekemolen Rebellion Lola-Toyota 3m31.866s
10. P1 Ara/Minassian/Bourdais Pescarolo Dome-Judd 3m33.066s
11. P1 Brabham/Chandhok/Dumbreck JRM HPD 3m35.421s
12. P1 Montagny/Baguette/Kraihamer OAK Pescarolo-Judd 3m35.584s
13. P1 Collard/Boullion/Hall Pescarolo-Judd 3m37.485s
14. P2 Martin/Charouz/Graves ADR ORECA-Nissan 3m38.181s
15. P2 Nicolet/Lahaye/Pla OAK Morgan-Judd 3m38.598s
16. P2 Panciatici/Ragues/Rusinov Signatech ORECA-Nissan 3m39.152s
17. P2 Beche/Thiriet/Tinseau TDS ORECA-Nissan 3m39.252s
18. P2 Perez-Companc/Ayari/Kaffer Pecom ORECA-Nissan 3m39.711s
19. P2 Firth/Hughes/Hartley Murphy ORECA-Nissan 3m39.877s
20. P2 Heinemeier Hansson/Leinders/Martin OAK Morgan-Nissan 3m39.899s
21. P2 Sims/Buurman/Iannetta Status Lola-Judd 3m40.280s
22. P2 Potolicchio/Dalziel/Kimber-Smith Starworks HPD-Honda 3m40.471s
23. P2 Briere/Petersen/Nakano Boutsen ORECA-Nissan 3m40.727s
24. P2 Ordonez/Brundle/Brundle Greaves Zytek-Nissan 3m40.738s
25. P2 Dolan/Hancock/Kurosawa Jota Zytek-Nissan 3m41.287s
26. P2 Mailleux/Lombard/Tresson Signatech ORECA-Nissan 3m41.982s
27. P2 Tucker/Bouchut/Diaz Level 5 HPD-Honda 3m42.224s
28. P2 Zugel/Gonzalez/Julian Greaves Zytek-Nissan 3m42.292s
29. CDNT Franchitti/Krumm/Motoyama Highcroft Delta Wing Nissan 3m42.612s
30. P2 Frey/Hirschi/Meichtry Race Performance ORECA-Judd 3m43.619s
31. P2 Holzer/Schultis/Moro Kodewa Lola-Lotus 3m45.664s
32. P2 Giroix/Johansson/Badey Gulf Lola-Nissan 3m47.244s
33. P2 Haezebrouck/Thirion/Rosier Extreme Limite Norma-Judd 3m48.025s
34. GTE P Makowiecki/Melo/Farnbacher Luxury Ferrari 3m55.393s
35. GTE P Fernandez/Mucke/Turner Aston Martin 3m55.870s
36. GTE P Gavin/Milner/Westbrook Corvette 3m55.910s
37. GTE P Bertolini/Beretta/Cioci AF Corse Ferrari 3m56.484s
38. GTE P Taylor/Garcia/Magnussen Corvette 3m57.181s
39. GTE A Neiman/Pilet/Pumpelly Flying Lizard Porsche 3m57.594s
40. GTE P Lieb/Lietz/Henzler Felbermayr-Proton Porsche 3m57.606s
41. GTE P Alfaisal/Curtis/Edwards IMSA Porsche 3m58.035s
42. GTE P Bergmeister/Long/Holzer Flying Lizard Porsche 3m58.717s
43. GTE A Simonsen/Nygaard/Poulsen Aston Martin 3m58.725s
44. GTE A Ehret/Montecalvo/Jeannette Luxury Ferrari 3m58.800s
45. P2 Rostan/Ihara/Deletraz Gulf Lola-Nissan 3m58.895s
46. GTE A Ried/Roda/Ruberti Felbermayr-Proton Porsche 3m59.181s
47. GTE A Bornhauser/Canal/Lamy Larbre Corvette 3m59.192s
48. GTE P Walker/Cocker/Wills JMW Ferrari 3m59.638s
49. GTE P Fisichella/Bruni/Vilander AF Corse Ferrari 4m00.025s
50. GTE A Perazzini/Cadei/Griffin AF Corse Ferrari 4m00.288s
51. GTE A Armindo/Narac/Pons IMSA Porsche 4m00.332s
52. GTE A Kauffman/Aguas/Vickers AF-Waltrip Ferrari 4m00.691s
53. GTE A Krohn/Jonsson/Rugolo Krohn Ferrari 4m02.323s
54. GTE A Rodrigues/Ferte/Illiano JMB Ferrari 4m02.461s
55. GTE A Bourret/Gibon/Belloc Larbre Corvette 4m02.969s
56. GTE A Camathias/Daniels/Palttala JWA Porsche 4m03.661s