Albion's player of the season Pascal Gross got the only goal in a 1-0 victory that meant the Seagulls secured survival with two games to spare.
It was also a historic, first win in 35 years against United and came from a superb all-round team performance which produced wild scenes on the south coast at the final whistle.
Mourinho, whose team are chasing second in the Premier League, said that his side were unable to motivate themselves, despite him warning them that Albion would be going all-out for the three points.
He said: "Today, I think it was a clear difference in the desire to fight for targets. They had one target, to get the points and to celebrate their Premier League qualification for next season - so their survival.
"We have the target to get points, today three or one to finish second. They clearly showed that for them it was more important for them to stay in the Premier League than for us to finish second.
"I think since the first minute they showed how important it was for them and we didn't show that. We showed it in the first 20 minutes. There was a little bit of pride as we are losing and didn't want to lose.
"We probably deserved a goal as we had a couple of chances, but clearly there was a difference in emotion. Emotion is a bit part of the game. We were here ready to give everything and we weren't able to motivate ourselves."
The United boss added that Albion's 'big objective' was what drove them on and questioned his own players' ambition to finish as runners-up.
He said: "It's always disappointing as it's not me. If my players were honest and fair, which I think they want, if you ask them they will tell you for how long I spoke during the week, before the game and at half-time, trying to anticipate the scenario and persuade them the only possibility to have to compete against a team like them (Brighton) is if you have the same kind of commitment and ambition they have.
"For me it was proven that they were humble and fighting for their humble, but big objective, which was to get the points and finish the fight against relegation with success. We were not ready to prove that the second position is important for us. I am disappointed as second position is important for me, I am not sure if every one of my players is as disappointed. I'm not sure."