The Gunners centre-half netted an own goal which put Fulham ahead not long after the hour-mark but atoned for his mistake with a leveler eight minutes from time.
Arsenal conceded in calamitous circumstances in the 64th minute when Fulham skipper Danny Murphy chipped a ball into the area and as John Arne Riise bore down on it, Vermaelen hacked it into his own net as he attempted to clear with a swift left boot.
The Belgian was able to make amends inside the final ten minutes when he met Theo Walcott's teasing cross with a powerful header to save face for the North London club who have never lost at home to the Cottagers in their history.
Fulham keeper Mark Schwarzer made a crucial save in the sixth minute when Aaron Ramsey toe-poked on goal before Wojciech Szczesny produced a top-shelf block from Moussa Dembele's fierce drive four minutes before the break down the other end.
Gunners skipper Robin van Persie almost kept his scoring run rolling along when he turned and fired on his trusty left in the 59th minute but Fulham defender Chris Baird was well-placed on the line to keep it out after Schwarzer had been beaten.
Arsenal doubled Fulham's attempts on goal but were only able to breach Schwarzer late in the piece to record a draw that sees them replace Liverpool in sixth position ahead of their meeting with league leaders Manchester City tomorrow as Martin Jol's men moved up to 15th despite winning just one of their last six.