Their victory was the third meeting between the teams in quick succession after a 1-1 draw in the first match at Whaddon Road and last week's 4-1 home victory for the south coast club in the Johnstone's Paint Trophy.
They edged through to a trip to Torquay on a wet night at the Withdean but made heavy weather of it after dominating the first half.
Adam El-Abd gave them an 18th minute lead with a thumping header into the roof of the net from a corner to the near post by Dean Cox.
It was a collector's item - the first goal from a Brighton defender since El-Abd also scored with a header in the Carling Cup at Southend 14 months ago.
Brighton should have sewn the tie up by half-time.
Jake Robinson hit the base of a post from long range, George O'Callaghan curled narrowly over and Cheltenham's busy keeper Shane Higgs saved shots from outside the box by Cox and Andrew Whing.
It was one-way traffic in the opening 45 minutes, but Cheltenham almost snatched an equaliser on the stroke of half-time when Steven Gillespie's angled drive from eight yards was smothered by Brighton keeper Michels Kuipers.
Brighton failed to heed the warning and they were punished when the impressive Gillespie equalised in the 65th minute.
The Liverpudlian striker, released by Paul Connor, rounded Kuipers as the Brighton defence looked in vain for offside and finished calmly from a tight angle.
Brighton restored their advantage two minutes later, courtesy of a controversial penalty.
Referee Mike Russell ruled that Gavin Caines had impeded Nicky Forster and skipper Dean Hammond sent Higgs the wrong way from the resulting penalty.
Nicky Forster fired wide a further chance to put Brighton out of reach and they almost paid for their wastefulness with four minutes left.
A header by Shane Duff from an Alan Wright corner crashed against the underside of the crossbar.
The ball was driven back in for Connor to divert past a wrong-footed Kuipers, but an offside flag came to Brighton's rescue.