Goals from Inigo Calderon and Will Buckley helped Brighton extend their unbeaten run to three matches.
In a match lacking many clear chances, a goal in each half condemned the visitors to a second successive defeat.
Calderon opened the scoring with a brilliant curling effort from 25 yards on 37 minutes, leaving former England goalkeeper David James with no chance.
Buckley put the game beyond Bristol City in the 73rd minute when he rounded James to clinch victory.
Both sides had struggled against lower-league opposition in the third round of the FA Cup last weekend, with Brighton being held to a home draw by Wrexham, while City went down 1-0 at League Two side Crawley Town.
But there was little sign of a reaction from either side, with the game lacking any real verve or excitement.
Brighton could have been awarded a penalty midway through the first half when Craig Mackail-Smith tangled with Lewin Nyatanga in the penalty box and went to ground, but referee Keith Stroud remained unmoved.
The match was in desperate need for a moment of quality and it got it in the 37th minute through the Spaniard Calderon, whose sumptuous finish left James helpless.
Brighton shaded the second half, Buckley shooting over from 20 yards and Alan Navarro missing the target with a similar effort five minutes later.
The home side always looked the more likely to score again and Gus Poyet's side made sure of victory when, from Lewis Dunk's defence-splitting pass, Buckley skipped past James and rolled the ball into the back of the net.
The visitors had to wait until the final minute for their first and only effort on target, and even then Brett Pitman could not beat Peter Brezovan in the Brighton goal.
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Brighton manager Gus Poyet told BBC Sussex:
"I am pleased for many reasons today. Everyone knows we've got plenty of injuries and our captain suspended.
"Then we started the game and lost two more players but everyone was outstanding, everyone did their jobs. They did what we asked them to.
"This was our best performance for a while. We were solid, we passed the ball when we had to, we didn't take any risks we didn't have to and we scored two unbelieveable goals."