Paul Scholes sent United in the lead with a superb long range strike, but Simon Davies equalised.
Brede Hangeland scored both and own-goal and a goal for the hosts in the second half.
“In fairness they deserved a point,” Ferguson told Sky Sports. “They played very well in the second half.
“The first half belonged to us but they played better than us in the second half.
“When you have the lead and you have the opportunity to seal the game with a penalty you think you’re home and dry, but I’ve got to give credit to Fulham.”
Fulham keeper David Stockdale saved Nani’s spot-kick late in the second half and Ferguson believes it was a key moment in the game.
“The goalkeeper reacted quickly and you’ve got to give him credit, but I think it was a bad height,” he said.
