The Croatian forward was handed a two-match ban for diving in Arsenal’s 3-1 victory over Celtic last month.
Fergie said: “I have to agree that something had to be done”
Arsenal boss Arsene Wenger claimed it was wrong by Uefa to single Eduardo out.
Fergie added: “I agree with Arsene, I would ask the same question ‘is it going to happen to everyone?’
“You become insular and protective of your own player and own team, we’re all selfish that way.
“I would have been saying ‘what about all the rest of the players?’.
“But I wouldn’t have been pleased if my player had done that.
“I wouldn’t say it publicly though, because when you do that you’re in danger of losing the morale of the dressing room.
“Privately, as I’ve done many times, you have a different view, but I wouldn’t do it publicly.”