United beat Ajax 2-0 in Stockholm on Thrusday (AEST) to claim the trophy and a priceless place in the group stages of the Champions League for next season.
Ajax captain Davy Klaassen accused United of "waiting to play long balls" during a match in which they comfortably kept the Dutch side's attack at bay while scoring goals through Paul Pogba and Henrikh Mkhitaryan.
It is not the first time Mourinho's side have been criticised in this season's tournament, with Celta Vigo striker Iago Aspas claiming his side were "infinitely superior" as they narrowly lost their semi-final tie 2-1 on aggregate.
But the United manager insisted that their tactics were justified given that they emerged with the trophy in hand.
"We always thought that we could win the Europa League and we are very happy," Mourinho told BT Sport. "We played intelligently, we did it in a comfortable way. We were much stronger than them.
"If you want to press the ball all the time, you don't play short. If you are dominant in the air you go long. There are lots of poets in football but poets don't win many titles.
"We knew where they were better than us, we knew where we were better than them, we tried to kill their good qualities and exploit their weaknesses. We did that very well from the first minute and we totally deserve the trophy."
Mourinho admits that this has been the most testing season of his coaching career, with United having been victorious in the Community Shield, the EFL Cup and the Europa League but falling well short of expectations in the Premier League.
However, the former Chelsea and Real Madrid boss says it is more gratifying to have qualified for the Champions League by winning a trophy than through a top-four finish and is now looking forward to a long break.
"We preferred to reach the Champions League this way than finish fourth, third or second," he said. "We got the objective, we are back in the Champions League by winning a title, an important title. The club now has every title in world football. We fought hard for this since the beginning.
"We totally deserved the win. I am so happy to see the [injured] boys with the crutches with the trophy and now I am on holiday. I don't want to see any international friendlies, I am selfish. I can't do it.
"For me, enough is enough. It has been a very hard last few months, we were short of numbers.
"Three trophies in one season and the Champions League. I am very happy in my most difficult season as a manager. It is the end of a very difficult season but a very, very good season."