United guaranteed a top-four finish with a 2-1 defeat of Arsenal thanks to Marouane Fellaini's stoppage-time header, Arsene Wenger's side collapsing to a sixth straight away loss on his last visit to Old Trafford in charge of the Gunners.
Wenger named an inexperienced side, protecting star names for Thursday's Europa League semi-final with Atletico Madrid, but debutant Konstantinos Mavropanos impressed at the back and Ainsley Maitland-Niles shone in midfield.
Mourinho noted the lack of pressure on Arsenal's players contributed to a positive performance from Wenger's men, but the Portuguese was satisfied with the way his team responded to Romelu Lukaku's injury early in the second half.
"I think if it was a draw it wouldn't be unfair," Mourinho told Sky Sports . "I think they had a good game, no pressure for them, but they defended well - the two young centre-backs did very, very well.
"Of course, we were the team that tried to win, had more chances and tried to win in the last 20 to 25 minutes but that's normal, they had a positive game but we were stronger in the last 20 minutes.
"We changed our approach and had more width with [Anthony] Martial and brought on Marouane to compensate for losing Lukaku.
"We killed the Champions League story, we are there in the top four, but we still need four points to finish second.
"I knew they would drop into the block, normally 1-1 is a good result for them, without Lukaku they were more comfortable to drop the block as the Greek boy [Mavropanos] and [Calum] Chambers knew they would dominate Marcus [Rashford] in the air in the air, so we needed a second presence.
"Marouane scored a beautiful goal, in the end it mathematically qualifies us for the Champions League."
Before kick-off former United manager Alex Ferguson presented Wenger with a commemorative gift to mark his last visit to Old Trafford in charge of Arsenal.
Mourinho also warmly embraced the man he once called a "voyeur" and a "specialist in failure", although the Portuguese avoided joining Ferguson and Wenger in a touchline photo opportunity.
"I think we did it fantastically well as a club - because it was the club that did it - but I felt it would mean more Sir Alex coming down than myself," Mourinho said.
"I played against Mr Wenger three or four times here, the big rivalry between the two clubs was between them, so it was for Sir Alex to come."