Pearson was dismayed that his men gave away "soft goals" but insisted that defeat was tempered by the fact that they had set some high standards this season.
Leicester threatened a late comeback when Andy King rose unchallenged to head home from an Anthony Knockaert free kick to make it 2-1 - but Barnes netted his second from the penalty spot 13 minutes from time to clinch the points for Oscar Garcia's side.
The Foxes have now lost three of their last five games and Pearson said:"It is soft goals again. We let them in midweek (against Sheffield Wednesday) and again in this match.
"We've been the architects of our own downfall and it's happened in the last two games.
"We're not firing on all cylinders but the disappointment is tempered with the way we have been setting some high standards this season."
Leicester conceded their third goal when skipper Wes Morgan nudged the back of Barnes, and Pearson complained: "The penalty looked soft to me but these things happen.
"At 2-1,there was a possibility of us getting back into it as we created some chances.
"Well done to Brighton,they are a good side, but we didn't play up to the level we would expect. We didn't do it for the entirety of the game."
Garcia felt his whole team deserved credit after the Seagulls clinched their fourth win in the last six games.
Brighton's head coach considered the first half showing in the midweek defeat against bottom of the table Barnsley as the worst of the season by his side.
However, he was delighted to report a notable improvement when the leaders came to town.
The Spaniard said: "I want to mention all the players, not just one.
"On Tuesday it was our worst first half, today maybe it's the best first half at home.
"In this league you have to fight for every ball if you want to win a game.
"The atmosphere was very noisy. We wanted to start well and we wanted to be brave and we did it."
Garcia has no wish to talk up the Seagulls play-off challenge at this stage and insisted: "My players don't hear about the play-offs from me - they only hear from me about the next game.
"It will be a mistake for them to think of the play-offs.The time for that is at the end of the season or a month before."
Brighton's victory was achieved with them losing goalkeeper Tomasz Kuszczak with a stomach muscle injury in the warm-up, before skipper Gordon Greer was forced off early on with a calf problem.
Garcia added: "The difference between this game and when we played Barnsley was that we started really well.
"I wanted to start like this,we wanted to show a reaction and we did it.
"We have had a lot of injuries this season and it's not easy, but I'm happy with how we're managing it."