United struggled to create much against Chris Hughton's impressive visitors and their 66th-minute goal came via a huge deflection, with Ashley Young's shot looping in off Lewis Dunk.
Mourinho, whose second-placed team closed the gap between themselves and Premier League leaders Manchester City to five points, said afterwards: "It was a battle.
"It was a battle because Brighton were very good. I think they were good from minute one until the last minute. Good approach, defensively very well organised.
"I keep saying to defend well is very important. For some pundits no, but to defend well is very important. And they defended very, very well, and they were quite dangerous on the counter-attack.
"I think they played really well and we didn't play well.
"Today our creation was poor. The three players who played with (Romelu) Lukaku, they didn't get the ball, they were not successful in the one against one. Marcus (Rashford) did not have a happy match at all."
The Portuguese has endured criticism of his playing style and his comment about "some pundits" came a day after United great Eric Cantona told the BBC he was more of a fan of City boss Pep Guardiola's brand of football than Mourinho's "defensive way" and would "prefer to have him (Guardiola) as manager of Manchester United.''
Mourinho did have some positive words regarding his team's effort against Brighton, saying: "The good thing for me was the intensity got higher in the second half in search of the goal. Then after the goal we couldn't kill the game.
"In the last 10, 15 minutes I saw a humble team with everybody trying to play for the clean sheet and giving everything. So I am happy with the attitude."
He then went back to lauding promoted Brighton, saying: "I have to praise a team and a manager who a few months ago were playing in the Championship.
"Today they came to Old Trafford and they were the team until now who gave us the biggest problems."
When the goal came, it was from a disputed corner that the ball fell to Young.
Mourinho said he had "no idea" whether the corner had been correctly awarded, but Hughton was convinced Lukaku had touched the ball last and it should not have been given.
"I think when you see it again, it is not a corner," said Hughton, whose side remain ninth.
"It was a fortuitous goal. But I thought even after that, we tried to get back in the game. It wasn't to be in the end."
Mourinho's praise for Brighton was welcomed by Hughton, who said: "It's always very nice to hear that from the opposition manager but I am still incredibly disappointed because I felt we deserved to get more from the day.
"Certainly as an away team I felt we were value for a point."