Both Nani and Young failed to make the bench for the UEFA Champions League last-16 encounter at the Bernabeu on Wednesday, which ended in a 1-1 draw ahead of the second leg at Old Trafford in three weeks' time.
The snub struck another blow to out-of-favour Nani, who was fallen down the pecking order at United to fuel talk of a summer exit.
Ferguson admits it was a tough call to make, saying in the Daily Express: "There were a lot of disappointed players.
"Nani and Ashley Young - international footballers - I found it hard to explain to them I was leaving them out."
Another player to miss out was unused substitute Javier Hernandez, with Ferguson preferring top scorer Robin van Persie up front, with Wayne Rooney in a deeper role.
But the boss says chances will come for the Mexican frontman, nicknamed 'Chicharito'.
He added: "I explained to Chicharito that Robin van Persie is our main striker and we wanted someone to join in from a deeper position.
"Whenever Chicharito plays, he delivers. He has 14 goals, he will score more than 20 and will have opportunities."
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