The Chilli Boys settled quickly into the game and showed their status as a professional side with the third-tier struggling to get into gear early on.
It was no surprise that they took an early lead through Ayabulela Konqobe who capitalised on Linda Mntambo’s free-kick to finish off at the back post after 14 minutes.
Minutes later, they nearly found a second when Thabo Rakhale controlled inside the box, but saw his half-volley blocked on its path to goal.
They finally got their second after Mntambo was played in by Rakhale to finish off in the top left corner on the half and hour mark.
The best they could bring to the table was shots from range that failed to pose any problems to Brighton Mhlongo.
In the closing stages, chances flew in at either ends forcing both goalkeepers in particular Mhlongo to come up with two telling saves to keep their two-goal deficit intact.
Sizwe Mdlinzo was denied his debut goal with a point-blank save after beating two defenders, as they went into the tunnel with a two-goal lead.
The ABC Motsepe League side started the second half a lot brighter and asked a few serious questions of Teboho Moloi’s side.
However, they still found it difficult to break down the seventh-place Premiership side who regardless still controlled the game.
Moloi looked to shut up shop as early as the 56th minute with the introduction of Christopher Bergman, who replaced new signing Luis Miquissone.
After completing his duties, Rakhale was replaced by Maselaelo Seanego, while Andile Mbenyane followed later on in their third and final change.
With time running out, the Eastern Cape side gradually searched for more goals but found it tough to get any openings.
Meanwhile, it was Mhlongo who was called to action to deny Elliot Nana from getting his name on the score-sheet.
A defensive mix-up presented Mntambo the opportunity to secure his brace, but he failed to capitalise on the invited opportunity, as Chippa advance comfortably to the next round.
In another Nedbank Cup clash, Steenberg United booked their spot in the Last 16 with a 3-1 win over Orbit College.
Young Stars: Baloyi, Canga, Mahlangu, Seete, Nkadimeng, Hlatshwanyo, Kekane, Mdaka, Mathebula, Msibi, Nana
Subs: Malatji, Nsimbi, Mtimkhuku, Mashego, Lubisi, Nkosse, Mahlakoane.