Rooney was left kicking his heels on the bench for the first 70 minutes of the 2-1 reverse and was only introduced once the Red Devils had fallen behind.
The Manchester United striker went on the blaze over from close range in the latter stages as his side fought furiously to save their European skins.
With Ferguson opting not to attend the post-match press conference and the aftermath of the tie dominated by Cuneyt Cakir's controversial decision to dismiss Nani, forensic discussion of Rooney's omission will have to wait until nearer the weekend, when the United boss is next due to address the media.
However, to Mourinho's mind, given Ferguson is in line to win a 13th Premier League title this season, to add to his two Champions League trophies and other silverware, there should be no questions at all.
"Sir Alex has won the right for every decision to be correct and never have a question mark against them," said Mourinho.
"He is the best. He is the top. You (reporter) are nobody to put a question like that. I am nobody. He did a great job."
It is hard to argue that Ferguson got the call wrong given the two men who profited most from Rooney's omission, Ryan Giggs and Danny Welbeck, were two of United's better performers.
Nevertheless, there is now bound to be speculation over the England man's future.
The last time Real Madrid came to Old Trafford, Ferguson left out David Beckham.
And though - like Rooney - the midfielder was eventually introduced, he left United that summer.
Ruud van Nistelrooy was also ushered out after being omitted for a big game and former skipper Roy Keane - booted out mid-season in even more brutal fashion - is amongst those who feel the writing is now on the wall.
Rooney has already been linked with Paris St Germain recently, and came close to joining Manchester City when he slapped in his transfer request two seasons ago.
The next move is awaited with interest, particularly as United now have a tough FA Cup quarter-final to prepare for against Chelsea on Sunday.
"The decision was tactical," said United assistant-boss Mike Phelan.
"In that dressing room, everyone was fit. But big decisions have to be made. Tonight we had the balance just right."