The veteran striker continued his excellent season with his first United hat-trick leading his team to a 3-0 win in the Europa League last-32 first leg on Thursday.
While Mourinho was happy for the Swede, he was most pleased with the clean sheet his team kept at Old Trafford.
"He has scored so many hat-tricks in his career but this is a first for Manchester United," the Portuguese tactician told MUTV.
"We know that it is more difficult in England, we know clearly that it is fantastic for him.
"But the important thing is the result and the important thing is that we managed a clean sheet at home, which is important, and to score three goals is a good advantage for us.
"We can try to manage with that."
Ibrahimovic has scored an impressive 23 goals in 35 appearances in all competitions for United this season.
His latest display has his team in control of their tie against Saint-Etienne ahead of the second leg in France on Wednesday.