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 to blaze over from close range in the latter stages as his side fought furiously to save their European skins, and Mourinho says there should be no questions about Ferguson's decision to leave him out.
"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 Ferguson got the call right given the two men who profited most from Rooney's omission, Ryan Giggs and Danny Welbeck, were two of United's better performers.
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."