The striker was named on the bench as the Red Devils lost Saturday's FA Cup final 1-0 to his former club Chelsea, a first-half Eden Hazard penalty the difference between the sides.
The result means Manchester United will finish the season trophyless, and also snapped Mourinho's perfect record in English Cup finals.
And Mourinho, who named Marcus Rashford as his starting striker in Lukaku's absence and gave the Belgium international 20 minutes off the bench, said it was not his choice.
"It's not difficult, it was his decision, it was his decision," Mourinho said at a post-match news conference.
"I knew the opponent I was going to play against and I knew they have a compact low block with lots of physicality where they try to close everything.
"I knew that without a target man it would be difficult for us. I know at least [it would have helped having Marouane] Fellaini coming from the second line, attacking their defence with his physicality.
"I knew that would be difficult, but I wouldn't expect that the game was exactly like it was because I think it was a bit too much.
"When a player tells you he's not ready to play, not ready to start, then the question is, 'How many minutes you think you can [play]?' But how can I convince a player who is not ready? It's nonsense."