The win was Arsenal manager Arsene Wenger’s first in 16 competitive meetings with United boss Mourinho.
“I left Highbury and they were crying, I left Emirates and they were crying,” Mourinho said of past games at Arsenal.
“Finally today they sing, they swing the scarves. It’s nice for them.”
He added: “It is the first time I leave and they are happy. Before they were walking the streets with their heads low.
“The Arsenal fans are happy and I am happy for them.”
Wenger’s only previous win over Mourinho came in the 2015 Community Shield, when the Portuguese was in his second spell at Chelsea.
The managers first met in December 2004 – when the Gunners were still playing at their former ground Highbury – in a 2-2 draw.
“To have that record of winning so many matches is not normal. Normal is win, lose, draw,” Mourinho said.
“Do you think I enjoy the fact a big club like Arsenal is not winning trophies? I am not enjoying that. It’s a big club.
“Wenger is not a small manager. He is a big manager. So it’s not normal and I really don’t care about it.”
Sunday’s defeat leaves United four points behind rivals Manchester City in fourth place, and five points from Liverpool in third, albeit with a game in hand over the Anfield club.
However, with a spot on offer to the winners of the Europa League, United could finish outside the top four and still qualify for the Champions League.
United conclude their Europa League semi-final against Celta Viga at Old Trafford on Thursday, having beaten the Spanish side 1-0 in the first leg on Thursday.
“We want to try to win the Europa League – it’s more important than finishing fourth. I think it will be almost impossible to qualify through the Premier League,” Mourinho said.
“Trophies make history. Not league positions. We go with everything to get into that final.
“Thursday is the match of the season. I hope Old Trafford feels the same, because we need Old Trafford.”