His scorching left-foot shot made him the first player to score for both sides in successive matches and briefly ignited Swindon's hopes of avoiding the drop.
They were in front for almost 20 minutes until a neat back-heel by David Noble put young David Cotterill in for City's equaliser.
A clever goal it was too, bent wide of keeper Rhys Evans' left hand.
A derby strangely lacking in passion now came to life as a draw was of no use to either side.
But six minutes of added on time brought about by an injury to Swindon's Steve Jenkins failed to separate the sides.
Only a win could save Swindon and, aware of the need, they arrived with four changes and an attacking intent.
They won seven corners in the first half and saw Chris McPhee drive left-footed over the top.
A niggly relationship developed between McPhee, one of two Brighton players on view - Mark McCammon of City was the other - and central defender Louis Carey.
When it became too physical referee Keith Hill had a lengthy lecture for McPhee but Swindon were not finding the firepower needed in front of goal.
City too took a long time to settle and when they shaped to break through found Evans on top of his game.
The Swindon keeper though twice rode his luck. He was left flat-footed when Noble took a punt at a loose clearance.
Then, from an Alex Russell free-kick, a Liam Fontaine header looked certain to put City in front until Steve Jenkins somehow cleared off the line.
City though were so nearly caught out when Gareth Whalley surged through the midfield and then no-one got in a challenge when Brown broke through on the left for his goal early in the second half.