The Manchester United boss, who previously blasted players for being cautious with injury, admits his side desperately needed their target man.
He said: “When a player tells you he's not ready to play, that he's not ready to start the game, then the question is how many minutes do you think you can play him.
“How can I convince a player that is not ready to play?”
Lukaku was crocked with an ankle injury three weeks ago against Arsenal and has been doing his rehab in Belgium.
He has been wary of rushing back and risking his World Cup fitness – and told United he was not fit to start in the defeat to Chelsea.
CHELSEA 1 MAN UTD 0 Hazard first-half penalty seals FA Cup glory for Blues at Wembley
Mourinho said: “It's not difficult decision. It was an easy decision.
“I knew the opponent I was going to play against. I knew they have a compact low block with lots of physicality where they try to close everything.
“I knew without a targetman it would be difficult for us, or Marouane Fellaini coming from the second line, attacking their second line with his physicality it would be difficult.”
“He made a decision of not being ready to start but maybe ready to give us a little help.
“So, one thing is to start the match and to play for 90 minutes. Another thing is to be on the bench and play a few minutes and that is what he told us he would be ready to do.”
Marcus Rashford started against Chelsea, who won through Eden Hazard’s penalty, and Lukaku came on for the last 17 minutes.
Mourinho insisted Chelsea won with long-ball tactics and his team were unlucky.
He added: “I think our team did a fantastic defensive job without defending. We controlled positions, transitions really well.
“They only played long balls to Giroud to flick., When you play against a team so predictable it's quite easy to adapt to it.
“I thought we wouldn't concede any goal in this match. But of course Hazard is a very good player and he created a penalty.
“My opinion on my team's performance is that every defeat hurts, but for me personally the ones that hurt less is when you give everything and you go without any regrets.
“I prefer to lose like today than lose like we did at, for example, Newcastle. I leave my players happy with them. For me that's really important.”
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