The match started at a frantic pace from both sides as they battled for possession and dominance following a delayed start at the DHL Stadium due to large number of supporters not making the 15h00 kick-off time.
In the 14th minute new Amakhosi striker Khanyisa Mayo came closest to scoring when his curling shot hit the outside of upright following good pressing from the Chiefs forwards.
Stellenbosch midfielder Genino Palace tried a tame shot that was saved by Fiacre Ntwari 35th minute but a physical battle ensued which saw 18 fouls and one shot on target for each side ahead of half-time.
In the 61st minute an accidental collision between Stellies goalkeeper Oscarine Masuluke with an onrushing Khanyisa Mayo ensued. This occurred after the keeper made a one on one save from the latter which led to the former Baroka keeper being substituted for captain Sage Stephens.
The two teams failed to retain possession and were prone to having to attempt long range efforts in order to try and break the deadlock but failed to do so until regulation time ended.
Extra-time resembled the same pattern despite an early red card to Stellenbosch defender Thapelo Mokobodi in the 106th minute, shortly after the first stanza of extra time.
Amakhosi could not seize the numerical advantage over the resilient Western Cape side leading to the inevitable penalty shootout at the DHL Stadium.
Stellenbosch substitute Andre de Jong missed the opening spot kick of the shootout but misses from Kaizer Chiefs' Western Cape-born duo Tashreeq Morris and Dillan Solomons condemned the visitors to a Round of 16 exit.
The result ends Amakhosi's three match unbeaten run and Stellenbosch's run of six matches without a victory.
Orlando Pirates clinched the Carling Knockout Cup in dramatic fashion at the New Peter Mokaba Stadium, edging Marumo Gallants 1-0 after extra time to secure their second trophy of the season.
Marumo Gallants' goalkeeper Washington Arubi says his side is comfortable being labelled the underdogs ahead of Saturday's Carling Knockout final against Orlando Pirates.
Kaizer Chiefs winger Asanele Velebayi says his early months at the club have been a steady, game-by-game learning process as he finds his feet in the top flight.
Kaizer Chiefs co-coach Khalil Ben Youssef has admitted his side continues to struggle in front of goal but insists the team is working hard to solve the problem ahead of Sunday’s clash with TS Galaxy in Mbombela.
