Saturday's result left United second on 29 points from 13 games, five behind City who visit Huddersfield Town on Sunday but Mourinho congratulated Brighton rather than his team who looked devoid of pace and creativity.
"I want to be honest and give them (Brighton) what they deserve, for me probably they deserve more than the result they got," Mourinho told the BBC.
"I think we were more spirit and heart than quality. Sometimes to play with too many attacking players doesn't mean you are offensive. We had a lot of attacking players on the pitch but we lost a bit of control in midfield."
It took a Lewis Dunk own goal in the 66th minute to settle an uneventful contest after United's 32-year old wing-back Ashley Young let fly from the edge of the penalty area and the ricochet left keeper Mathew Ryan rooted to the spot.
Brighton's packed defence had foiled waves of attacks by United's 4-2-3-1 formation, with Anthony Martial and Marcus Rashford deployed either side of playmaker Juan Mata and behind lone striker Romelu Lukaku.
United missed their best chance on the stroke of halftime, when Ryan denied Lukaku and Paul Pogba with a double close-range save after Brighton had launched several darting raids down the right flank.
But the visitors failed to clear a corner when United seemed to be running out of ideas and the home side took advantage with Young unleashing a shot with his weaker left foot.
Having heaped more praise on Brighton, Mourinho also gave his team some credit for grinding out a result after Wednesday's 1-0 defeat by Swiss side Basel in the Champions League.
"We played amazingly well in the first half against Basel and we lost so the most important thing are the points.
"We had amazing chances a couple of days ago and we couldn’t score, today we did it," he said.
"Congratulations to them (Brighton) for their performance, congratulations to my boys. My boys they didn’t play well but they gave everything and they don’t deserve bad words from me."
(Writing by Zoran Milosavljevic; Editing by Ian Chadband/Rex Gowar)
