The visitors saw a five-match unbeaten run brought to an end as Steve Sidwell's strike and a penalty from Dimitar Berabtov secured a first win for new Fulham boss Rene Meulensteen.
Villa rarely threatened in a game dominated by the hosts, but they had reason to feel aggrieved after seeing Fulham awarded a dubious penalty following a collision between Leandro Bacuna and Alexander Kacaniklic.
And the away side's misfortune was summed up in the closing stages as referee Mike Dean refused to point to the spot, despite Aaron Hughes' clumsy challenge on Villa attacker Gabriel Agbonlahor.
The Scot disagreed with both of Dean's penalty calls, but admitted that his team did not perform well.
"I don't think we did enough to win the game," Lambert said. "I am disappointed with some of the decisions, the two penalties for instance.
"I've just spoken to Mike, he had his views on it, mine is different from his. I think if you give a penalty you've got to be 100 per cent sure.
"I think the lad has actually back into Leo [Bacuna]. In Gabby's one Gabby has got a foot on it first.
"As a team, we were short. We never got going. But we pick ourselves up and go again."