The Red Devils went down 5-4 in a thrilling encounter at Stamford Bridge after the hosts forced extra time with an Eden Hazard penalty in injury time.
Nani gave the ball away at the death to allow Chelsea to craft the move that led to their spot kick, but Ferguson refused to criticise the winger.
"Nani tried to beat a player, lost the ball and we've got a penalty against us. I don't know if it was a penalty or not but at that point think the young players started to feel it," BBC Sport quotes Ferguson as saying.
"If you are winning 3-2 in the final seconds of the game then you should see it out. Nani is an individual. He wants to beat men and we are not going to discourage that."
Ferguson also drew positives from the defeat, insisting that his side played some good football and hailing the impact of veteran Ryan Giggs.
"Some of our football was terrific. Ryan Giggs played the full game and he is 39 next month," he added. "He is an example to all the players on that pitch, including the Chelsea players."
Chelsea will visit Leeds United in the quarter-finals.