Agbonlahor had been due to start Saturday's Premier League clash at Villa Park, but was forced to withdraw in the warm-up, with Andreas Weimann taking his place in the XI.
Villa went on to lose 2-0 as late goals from Yaya Toure and Sergio Aguero put the seal on a third consecutive defeat after previous reverses at the hands of Arsenal and Chelsea.
With the Premier League taking a break due to the upcoming international fixtures, Agbonlahor has a fortnight to recover before Villa are next in action at Everton on October 18.
"In the warm-up he came in and he didn't feel well at all," Lambert said.
"The doctor saw him and sent him home. We'll see how he is on Monday.
"You run the risk if you play somebody who's not well, especially in that magnitude of a game.
"It was a blow because Gabby's speed is a major point for us. I thought Andy [Wiemann] went in there and did well.
"It threw me off guard because I didn't know until he came in that he wasn't feeling well."
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