Goals from France global Pogba and Armenian Henrik Mkhitaryan in each half gave United their first European trophy since 2008, and their first Europa League crown. Strong defensively and a powerful presence in midfield, Pogba took the match by the scruff of the neck early on and was rewarded with a goal, albeit deflected, after 18 minutes.
The match was overshadowed by Monday's terror attack at the Manchester Arena, which killed 22 people, and a minute's silence was observed before kick-off in front of a boisterous but respectful crowd at Friends Arena.
But his celebrations at the end of a 63-game season for United demonstrated just how much the Europa League victory meant to him.
Yet hope was soon dampened as within minutes Ajax's first major European final in 21 years became an uphill battle.
Marouane Fellaini came close to a third goal for United, but his header from Pogba's delicious cross went straight at Andre Onana.
Mourinho, a UEFA Cup victor with Porto in 2003 and two-time European champion, has now won all four of the major European finals he has contested.
"It was very special because of the events that happened in Manchester and now they qualify for Champions League", he said. We were unable to play our own game.
The Dutchman, 19, was challenged by manager Jose Mourinho to prove his fitness against Crystal Palace on Sunday to be in with a chance of making the squad in Stockholm.
However, two goals proved enough for Mourinho's men on a hard evening. Of the Dutch side's 17 shots on goal, only three were on target.
Armed police patrolled the perimeter of a ground that witnessed United's 64th match of a draining campaign, with the Europa League taking them more than 15,000 miles.
The win can also be seen as a sign that United may finally be recovering from the retirement of Sir Alex Ferguson in 2013. "But if we could, we'd change the peoples' lives for this cup". The boringness of the match obviously doesn't and shouldn't bother United though, since the victory was all they were after and they got it.