Paul Pogba's deflected shot put them ahead in the 19th minute and Henrikh Mkhitaryan's sixth Europa League goal of the campaign, flicked in from Marouane Fellaini's header at a corner, confirmed they would add to the EFL Cup won against Southampton earlier this season.
Wayne Rooney made a brief appearance as a substitute with a minute of normal time left and the game won, being handed the captain's armband by Antonio Valencia on what could well be his farewell appearance for United.
And as the final whistle sounded and United's celebrations began, chants of "Manchester" rang around the Friends Arena in tribute to those who died and were injured in the attack which cast a shadow over this showpiece occasion.
It means United are now the fifth team to claim the full quota of European trophies, joining an illustrious list with Ajax, Chelsea, Juventus and Bayern Munich.
Like this United side, there is still much to do before he can be regarded as the finished article but the manner in which he made sure early midfield dominance was secured was impressive and he added a goal for good measure.
It may end up being classed as an own goal but Pogba will happily accept it, trying his luck from 20 yards after being afforded just a little too much space by Ajax captain Davy Klaassen and helped by a huge deflection off Davinson Sanchez. And perhaps he was due that touch of good fortune after being thwarted by the woodwork so often this season.
And it was another profitable night for another big-money Mourinho buy, Mkhitaryan. The Armenian struggled in the first half but showed what a priceless poacher's instinct he has, swooping from close range for another Europa League goal.
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