Jimmy Bullard scored the winner with five minutes to go after Simon Davies lashed in an equaliser.
Scott Carson did his England chances no good as the shots on target to goals ratio again showed a 100% record. Two shots two goals.
The game was at times a torrid affair as both sides struggled to create any real opportunities. Villa were clearly missing the influence and deliveries of winger Ashley Young and often aimed long to John Carew.
Their cause was disrupted by the injury to Gabby Agbonlahor just before half time. The England striker was scythed down by Simon Davies who didn't even receive a yellow card.
Agbonlahor was replaced by Marlon Harewood, which places doubts over his place in the national team for Wednesday night.
He did have a good opportunity shortly before going off but he couldn't connect with a good low ball into the box.
Shaun Maloney, who replaced the suspended Young, tried hard to create and had a couple of wayward efforts.
The start of the second half saw an increase in tempo from both teams but they were still creating little.
That was until Shaun Maloney looped a corner into the box which was flicked on by Olof Mellberg and the ball inadvertently hit Aaron Hughes.
It was reminiscent of Liam Ridgewell's own goal for Villa at St Andrew's as another old boy put the Claret and Blue ahead.
The similarities to the game against Blues ended there. Fulham came charging back and a low cross into the box was diverted in by Simon Davies. The Welshman was a thorn in Villa's side all afternoon and he was certainly prickly to the crocked rose in the Claret and Blue crown, Agbonlahor.
Prior to Davies' goal the away side could have taken a two goal lead through the ever reliable Martin Laursen. The big Dane was unmarked from a corner but volleyed over.
With time running out, the game looked destined for a draw. But, Curtis Davies decided to slide in rashly on Diomansy Kamara and the injury plagued Jimmy Bullard stepped up to take the free kick.
He powered it from 25 yards and it eluded Carson in the Villa goal. The keeper should have saved it but as he does all too often he dived under the ball. The keeper's inability to shot stop cost Villa again. Not a good game for Mr Capello to be watching.
The Italian will have been grimacing as he saw Agbonlahor go off injured, Davies and Carson make mistakes and Barry failing to exert his usual influence.
Fulham will be elated with a first win in 15 but it's back to the drawing board for Martin O'Neill. The Northern Irishman will know that an immediate bounce back is necessary against Newcastle next week.