Brightonâ€™s second league victory in seven outings moved them above opponents Barnsley on goal difference in the battle for the play-off places.
A twice taken penalty in the first half by Leon Knight decided a dour encounter at Withdean.
Trevor Benjamin, making his home debut from Leicester, escaped from Barnsley captain Peter Handyside before he was brought down in side the box by Craig Ireland.
Knightâ€™s first attempt was saved by the diving Tony Caig, but referee Ray Olivier ordered a retake because the keeper had moved off his line.
Knight made no mistake second time around, sending Caig the wrong way for his 19th goal of the season.
Benjamin almost doubled Brighton's lead early in the second half. His instant control and shot from a Kerry Mayo throw in forced Caig, on loan from Newcastle, into a fine stop.
Brighton had to replace goalkeeper Ben Roberts at half-time because of a back injury.
Michels Kuipers took over, the Dutchman's first appearance since a car crash in November.
Kuipers had little to do and Barnsley did not threaten an equaliser until a late rally.
Anthony Kay drove narrowly wide from outside the area with 15 minutes left, their first shot of the match.
The visitors had penalty appeals of their own rejected in the closing stages when sub Alex Neil was bundled over by Brighton replacement Gary Hart from a Kevin Betsy cross.
Brighton manager Mark McGhee said: "It was an important win for us. We are still not at our best, but we totally dominated the game." Barnsley boss Gudjon Thordarson, who has just agreed a new one year rolling contract, said: "I have no complaints about the penalty Brighton were awarded, but it was hard on Tony Caig to be penalised after saving it."