A deflected Paul Pogba strike and a goal from Henrikh Mkhitaryan gave the Red Devils a 2-0 win over Ajax in an emotionally-charged final at the Friends Arena in Stockholm on Wednesday evening.
The win means that the Premier League side have secured a place in the Champions League next season and means that Mourinho has won two trophies in this first season at Old Trafford.
Following the final, a group of UEFA technical observers that included former United boss Sir Alex Ferguson have selected an 18-man squad containing the top performers from the tournament as whole, with Manchester United players filling also half of the slots.
Sergio Romero was given the nod ahead of David De Gea in the tournament this year and his excellent performances meant his was included in this squad of the season, with defenders Eric Bailly, Daley Blind and Antonio Valencia also making the grade.
Midfielders Ander Herrea, Paul Pogba and Henrikh Mkhitaryan were joined by Zlatan Ibrahimovic up front.
Ferguson was joined by fellow UEFA technical observers Cristian Chivu, Stefan Majewski, Mixu Paatelainen, Ioan Lupescu and Dejan Stanković in Stockholm to select the 18-man squad.
Europa League squad of the season
Sergio Álvarez (Celta Vigo), Sergio Romero (Manchester United)
Eric Bailly (Manchester United), Gustavo Cabral (Celta de Vigo), Jérémy Morel (Lyon), Matthijs De Ligt (Ajax), Daley Blind (Manchester United), Antonio Valencia (Manchester United)
Pablo Hernández (Celta Vigo), Ander Herrera (Manchester United), Paul Pogba (Manchester United), Youri Tielemans (Anderlecht), Corentin Tolisso (Lyon, Henrikh Mkhitaryan (Manchester United), Amin Younes (Ajax)
Zlatan Ibrahimović (Manchester United), Alexandre Lacazette (Lyon), Bertrand Traoré (Ajax)