The Seagulls sixth league defeat out of seven in front of their own supporters leaves them still deep in trouble, despite making six signings during the January transfer window.
Manager Micky Adams kept faith with the team beaten 4-2 at home by Peterborough four days earlier.
Woeful defending cost Brighton dear on that occasion and Adams' loyalty backfired as further lapses at the back helped Carlisle to two first-half goals.
The Brighton rearguard were caught asleep in the 24th minute when Graham Kavanagh played a quick free-kick to Lewis Neal.
The former Preston midfielder cut the ball back for Joe Anyinsah who was given time and space inside the area to pick his spot low into the far corner.
It was a particularly bitter pill for Brighton to swallow, since Anyinsah snubbed them after a loan spell and signed for Carlisle last month instead.
Carlisle doubled their cushion four minutes later with another simple goal. Kavanagh's free-kick from the right was met at the far post by centre-half Richard Keogh with a swivelling right-foot volley into the roof of the net.
Brighton's frustration was summed up by skipper Nicky Forster searching for his 200th career goal. The veteran striker went agonisingly close early on with a glancing header just wide of the far post from a cross by Craig Davies.
Then, as Brighton poured forward early in the second half, Forster was put clean through by Calvin Andrew, only to completely mis-kick on the churned-up Withdean pitch.
Brighton lost heart after that and Carlisle have now opened up an eight point gap between the teams.