Mourinho was impressed by the performance of Blackburn, but believes that his side were worthy winners and suggested that defeat was a better result for the hosts than earning a replay at Old Trafford.
"I think the attitude of every player was really good. When I have important players on the bench, I can try to make an impact. It depends also on their mentality and they were more than ready to come with the right attitude for the team," he told BT Sport.
"Blackburn were a good team, better than the Blackburn of the Championship. They had an amazing attitude and belief, they gave us a really good match and with a different attitude we would lose this match.
"I think we deserved to win, but I think Blackburn would also have deserved to go to Old Trafford. But this is better for them - now they can focus on the Championship."
Mourinho faces a trip to former club Chelsea in the quarter-finals of the competition.