Manchester United defender Bailly was sent off late on after a clash with Celta Vigo player Facundo Roncaglia.
It means the Ivorian will miss the Europa League final in Stockholm later this month.
And though Mourinho praised his defender’s performance, he was not happy with the naivety he showed.
He said: “I didn’t see the red card incident but Eric Bailly was phenomenal.
“The game was emotional for everyone. Some kept control better than others.
“Facundo Roncaglia is not new in these situations, Bailly was probably naive.
“We now lose a very important player for the final, and we don’t have many.”
Manchester United manager Jose Mourinho
United overcame the Spaniards thanks to the 1-0 lead from the first leg followed by last night’s 1-1 draw.
Marouane Fellaini scored United’s opener in the first half before an 85th minute equaliser from Roncaglia, who was then also sent off in the incident with Bailly.
United now face four games in 10 days with the season finishing on May 24 with the final against Ajax.
