Villa also surrendered the league's second-best form record - a run of five games without defeat - in lacklustre fashion.
Dimitar Berbatov demonstrated his commitment to the Fulham cause with a sparkling performance and was the lynchpin as Fulham ended a run of six straight league defeats, teeing up Steve Sidwell for a well-taken opener before coolly dispatching a penalty he had helped win.
But Lambert refused to take his players to task for their below-par performance, admitting his men looked "tired" in west London.
Lambert said: "I don't think we did enough to win the game.
"Where I'm disappointed is the penalty. I had just spoken to Mike Dean, my view differs from his. I don't know what anyone else thinks but I'll leave other people to talk about it.
"Gabby got a foot on it first, and it's moments like that that change the game.
"If you lose any game you're always disappointed, but you pick yourself up and go again."