Having missed out on Champions League qualification via the Premier League, United must beat Ajax at the Friends Arena to secure a return to Europe's elite competition.
Mourinho has made his priorities clear in recent weeks by resting players for league fixtures, but he claims United's injury problems left him with no choice.
"It was not a gamble. It was a simple decision," said Mourinho, who picked a team with an average age of 22 years and 284 days for Sunday's season-ending 2-0 home win over Crystal Palace.
"When we lost players in a period of 17 matches in seven weeks, it was the impossible job. It was not a gamble, just a consequence of our situation."
Mourinho won the UEFA Cup, as the Europa League was previously known, with Porto in 2003, but the two-time Champions League winner has been publicly dismissive of the competition in recent years.
Upon returning to Chelsea in 2013, Mourinho said of the tournament, which the London club had won the previous season: "I don't want to win the Europa League. It would be a big disappointment for me."
United's performances during this season's tournament suggest their players were not sure how much they wanted to win it either.
They lost their first two away games, against Feyenoord and Fenerbahce, needed extra time to beat Anderlecht in the quarter-finals and were given a scare by Celta Vigo in the semi-finals.
Now that the trophy is within touching distance, Mourinho has started to paint the tournament in a different light.
He has already masterminded a League Cup success and has suggested Europa League glory would mean United have had a more successful season than trophy-less top-four rivals like Manchester City and Liverpool.
In the words of defender Phil Jones: "People will say we've not had a good season, but would you rather finish second and win nothing or win two cups and be in the Champions League?"
Victory on Wednesday would enable United to complete their collection of trophies.
They can also become only the fifth club – after Juventus, Ajax, Bayern Munich and Chelsea – to have won the Champions League, the Europa League and the now defunct European Cup Winners' Cup.
The final will not, however, be a glorious homecoming for United's Swedish striker Zlatan Ibrahimovic.
He will watch from the stands, along with fellow injury victims Luke Shaw, Marcos Rojo and Ashley Young, after sustaining knee ligament damage during the semi-final second leg win at home to Anderlecht.
Mourinho has confirmed that Sergio Romero will continue to start instead of David de Gea in goal, while Jones and Chris Smalling are vying for the right to replace suspended centre-back Eric Bailly.
Ajax approach the game with none of the cloying pressure that United must contend with.
Peter Bosz's exciting young team have carried the club to a first European final since a 4-2 loss on penalties to Juventus in the deciding match of the 1995-96 Champions League.
Ajax won the previous season's Champions League and famous figures from their 1990s golden team have helped to restore the club to former glories.
Edwin van der Sar and Marc Overmars are on the board of directors, while Dennis Bergkamp is one of Bosz's assistants.
There is even an on-pitch link in the form of 18-year-old winger Justin Kluivert, son of Patrick, who scored the only goal in the 1995 Champions League final against AC Milan.
"I feel no pressure," says Bosz, a former midfielder capped eight times by the Netherlands. "Everyone dreams of these games, so there's no pressure, just a big opportunity.
"They have a bigger budget for sure and if they feel pressure because of that, then OK. We like to play good football and hope to win."