Crowd trouble was the definition of events at Danie Craven Stadium as Chiefs got past the hosts on penalties following a stalemate after extra-time.
The start of the match was delayed due to traffic congestion outside the venue and fans then broke a section of the fence as they squeezed their way into the grandstand.
There were crowd issues again when Ashley du Preez scored the equalizer for Chiefs before chaos broke out again at the end of the shootout after Itumeleng Khune saved two.
Stellenbosch then issued a statement noting that as organisers, the PSL, advertised the match as sold out at the 15 000-capacity venue two hours before the start.
They then apologized to those that were inconvenienced.
The PSL, through their prosecutor, Zola Majavu have now charged Chiefs – who had most of the fans in the stadium.
"This is a further DC update. I can confirm that charges were preferred against Kaizer Chiefs, and they will be appearing before the PSL DC this coming Thursday to answer to charges of spectator pitch invasion in their match against Stellenbosch FC.
"Once the DC has been finalised, I will provide with further details and the outcome thereof.
"In the intervening period there will be no commentary on this matter until it is finalized," says Majavu.