Cameroon midfielder Baleba scored his first goal for the Seagulls in the 19th minute before Simon Adingra doubled the lead at the Amex Stadium with another eye-catching effort.
Wolves improved greatly after Goncalo Guedes’ 44th-minute goal changed the game but were made to pay for their profligacy when Ferdi Kadioglu’s late finish gave Albion some breathing space.
Tommy Doyle revived hopes of forcing a penalty shootout with a shot under the crossbar in added time before the hosts held on to maintain their unbeaten start to the game under head coach Fabian Hurzeler.
Brighton made eight changes after Saturday’s frustrating 0-0 draw with Ipswich, while only Joao Gomes kept his starting place for Wanderers after Sunday’s 2-1 defeat to Newcastle.
Baleba, one of three Seagulls players to retain his place, opened the scoring in style in the 14th minute.
The 20-year-old dispossessed Gomes deep in opposition territory before leaning into the bottom left corner from distance and celebrating the historic strike with a cartwheel and a backflip.
Albion scored again nine minutes later but Yankuba Minteh was offside when he turned home after Evan Ferguson’s initial effort hit Jose Sa and headed towards goal.
Wolves striker Guedes forced Brighton goalkeeper Jason Steele to deflect his powerful strike on the half-hour mark before the visitors fell further behind a minute later.
Having been given time and space on the left wing, Adingra cut inside to fire into the bottom right corner from the edge of the D.
Hurzeler’s hosts looked set to progress to the next round but Wolves breathed new life into the game a minute before the break.
Rodrigo Gomes released Matt Doherty on the left and his cross back was deflected right-footed by Guedes via a deflection off Adam Webster.
After controlling the game for most of the first half, Brighton found themselves on the defensive after the restart.
Only Steele’s legacy prevented Gomes from equalising seconds into the second half, before Pablo Sarabia came close to connecting with Guedes’ low cross in the 59th minute.
Albion continued to live dangerously and endured more anxious times.
Jack Hinshelwood prevented team-mate Webster from scoring an own goal with a shot off the line before Guedes fired needlessly wide of the left post.
Brighton were left shaken in defence but eventually secured their place in the fourth round with five minutes remaining.
Wolves goalkeeper Sa could only parry Danny Welbeck’s initial effort and substitute team-mate Kadioglu was on hand to convert his first Seagulls goal.
The simple finish looked to have killed the game off but Doyle still had time to increase the tension by slotting home after Brighton had inadvertently lost possession in their own penalty area.
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