Steve Barker's men will now face Orlando Pirates in a repeat of last year's final.
Sekhukhune, needing to overturn a two-goal deficit, made a lively start. In the fifth minute, Keletso Makgalwa teed up Bradley Grobler, but the experienced forward failed to hit the target.
Grobler spurned two further chances in the first half as the home side struggled to convert their early pressure.
Stellies punished that wastefulness in the 22nd minute when Mthetheleli Mthiyani fired in a spectacular strike from range to extend the visitors' advantage in the tie.
Sekhukhune goalkeeper Renaldo Leaner then kept his team in contention, saving well from Devin Titus in the 36th minute, before Andre De Jong dragged an effort wide just before the break. The halftime whistle sounded with Stellenbosch 1-0 ahead.
The second half saw Stellenbosch continue to threaten, with Henri Stanic and Ibraheem Jabaar both testing Leaner.
Sekhukhune finally found a breakthrough in the 66th minute when Siphesihle Mkhize converted from Tsepo Matsimbi's assist, levelling the game on the night.
Grobler's frustrating evening continued in the 73rd minute as he blazed another chance over the crossbar.
Despite the late push from Sekhukhune, Stellenbosch held firm to secure a 1-1 draw and confirm their aggregate victory.