The Lowndes/Andrea Piccini/Michele Rugolo/Steven Wyatt 458 was 16th fastest on combined times after the two-part Thursday qualifying procedure, four places ahead of the Van Gisbergen/Rob Bell/Tim Mullen MP4-12C.
The top 20 from the 61 car field progress to Friday's 20 minute Super Pole hit-out.
The Lowndes Ferrari was as high as ninth quickest in the second session, where none of the top 20 managed to improve their earlier times.
The ultimate pace was set by the #77 Mac VDS BMW of Lucas Luhr/Markus Palttala/Dirk Werner, ahead of the #3 Christopher Mies/Frank Stippler/James Nash WRT Audi and the Andy Soucek/Kevin Korjus/Kevin Estre #99 ART McLaren.
The Richard Muscat-driven Black Falcon Mercedes will meanwhile line-up six places further back in 42nd after it failed to complete a flying lap in the second session.
Liam Talbot's Kessel Ferrari also endured a difficult day, just 60th quickest on combined times.
The busy schedule of Thursday track running had earlier seen single practice and pre-qualifying sessions.
Practice was shortened by more than 20 minutes after a crash from McLaren driver Alvaro Parente damaged the barriers at Turn 11, forcing the ART-run car out for the remainder of the day.