The Cumbrians came from a goal down to boost their bid for a play-off place and leave Brighton reflecting on a match they should have won.
The home side, playing into a strong wind and driving rain in the first half, thought they should have had a penalty in the 28th minute when Dean Cox was brought down just inside the box by David Raven.
Instead of awarding a spot-kick, referee Patrick Miller showed Cox his fifth yellow card of the season for diving, which means he is suspended for the glamour FA Cup tie away to West Ham.
Brighton put that setback behind them to go in front in the 37th minute. Jake Robinson, switched to the right wing in a re-shuffle, crossed for Joe Gatting to head his second goal in as many games.
Cox wasted a great chance to put Brighton further ahead shortly after the break when he sent a downward header wide of the target from eight yards out after a cross in by Kerry Mayo.
It was an expensive miss as Carlisle drew level in the 56th minute.
A cross by Kevin Gall was headed against the underside of the crossbar by Karl Hawley and Spaniard Zigor Aranalde fired in the rebound at the far post.
Robinson almost restored Brighton's advantage with an angled shot from 25 yards which swerved against the crossbar.
Brighton were ruing their luck once again with nine minutes left when Carlisle were awarded a penalty.
A free-kick was headed on by Danny Livesey and Hawley was tripped by Mayo. Hawley's spot kick was saved by Wayne Henderson but the ball broke for Neale McDermott to slot in the rebound.
Carlisle's only previous away win this season was also on the south coast at Bournemouth, who coincidently are Brighton's next opponents.