The visitors were kept at bay by the Seagulls until City striker Sergio Aguero made the breakthrough after 70 minutes and Lewis Dunk's own goal doubled the advantage five minutes later.
Brighton next go to 2015-16 champions Leicester, with boss Hughton taking the positives from a defeat that many were expecting to be much heavier.
"This is our first Premier League game and we were playing against the team some think might win the league," he said. "There will be bigger scorelines than this in some Man City games, because of the quality that they've got.
"It's a very disappointed changing room, which shows it means something to them and shows they know that for 70 minutes we were very much in the game.
"We gave a really good account of ourselves."