Lombardo, manager of City's elite development squad, took charge of the Premier League champions at Boundary Park with boss Roberto Mancini and the majority of his first team only recently back from their tour of the Far East.
England trio Joe Hart, Joleon Lescott and James Milner lined up alongside France pair Gael Clichy and Samir Nasri, with Nigel de Jong taking the captain's armband for the 2-1 defeat to the League One side.
"It's a big day," said Lombardo.
"It was important for those players to improve fitness. I think it is much more important than the result."
City found success during their Asian tour with a new-look 3-5-2 formation, a system in evidence once more following direct instruction from Mancini.
"I talked with Roberto last night before travelling back to Manchester and he asked me was it possible to play three at the back?" said Lombardo.
"I don't know which (formation) it will be in the Premier League. Some teams will play like us and some will play 4-4-2."
City are yet to begin their summer spending despite persistent links with the likes of wantaway Arsenal star Robin van Persie.
Nevertheless, Lombardo insists himself and the Etihad Stadium backroom staff are at ease with the situation at present.
"It is not strange," he added. "We have one month more to pick up our targets.
"I think we have time for that and we are also strong without new players.
"I don't know about new players in this month - it's not my job that one!"
Clichy's slack pass led to Robbie Simpson putting the Latics ahead after four minutes.
Out-of-favour striker Roque Santa Cruz equalised after half-time as City dominated for long periods, but Latics summer recruit Jonathan Grounds smashed home Connor Hughes' stoppage-time corner to settle an entertaining contest.
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