Yasin Ayari's 11th-minute goal, which followed a miscued clearance by City right-back Matheus Nunes, proved the difference at the Etihad.
City, who started the weekend top of the table, pressed hard for an equaliser but could not find a way through against a determined Brighton.
This loss came just a week after a 2-1 loss to Aston Villa ended City's perfect start to the league campaign.
"It's a very similar feeling that we had after the Aston Villa game," said Maresca.
"Unfortunately, we created enough to get some points but we didn't score. In this moment, it's like this.
"We are second in terms of goals scored in the Premier League so that means we are scoring," he added. "We are conceding silly goals and we can avoid that. Hopefully we can avoid that in the next game."
Brighton's victory, their first away win over City, came just days after they lost on penalties in the League Cup to Maresca's men at the Etihad on Wednesday.
Bart Verbruggen was inspired in the Brighton goal as the Seagulls, who have now beaten both champions Arsenal and City in the league this season, moved to within two points of top spot.
Brighton have never won a major trophy and their youthful manager, Fabian Hurzeler, tried to keep his side's feet on the ground by saying his sole concern was their next match.
"We are in a big process - a process where we go home now and analyse the game and take the right things out of it," said the 33-year-old German.
English Premier League
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"Then we try to prepare for Getafe. That's another big challenge for us in the Conference League, a different game. We only try to go from game to game."
City's defeat means Arsenal can go top if they avoid losing at Liverpool on Sunday.
But 10-time English champions City know their results on the field may count for little this season unless they can successfully overturn a guilty verdict on more than 100 charges of breaking Premier League financial rules.
City have appealed, but if that ruling is upheld they are likely to face a severe points penalty and possible relegation from the English top-flight.