Chiefs clicked into gear with two goals in as many minutes in the second half to seal their berth in the last 16 of the competition.
Substitute Lehlohonolo Majoro was involved in both the goals in the latter period, first as provider in the 69th minute and then scorer to seal the result.
Maintaining a narrow 1-0 lead up until that point, Majoro's pin-point cross left fellow substitute Lucky Khune with a simple tap-in header to make it 2-0 to Chiefs.
Two minutes later, Majoro poached an inept clearance from Stars keeper Wesley Fransman to give Chiefs a 3-0 lead with just over 25 minutes left.
All Stars, established in 2010, gave a good account of themselves for most of the game, and frustrated the Soweto giants.
Chiefs had a monopoly on possession, and territory, but their finishing was far from convincing.
After going a goal up just before the half hour mark, Chiefs did not capitalise on the momentum from the goal.
Chiefs unlocked the Stars defence from early in the encounter.
The AmaKhosi boasted near 80 percent possession in the first half and Bernard Parker was close to opening the scoring in the 11th minute.
Parker found himself in good position in the middle of the box, but his headed attempt sailed over the crossbar.
Chiefs found their rhythm quickly and started creating a number of chances which they missed.
In the 27th minute Chiefs found the net with long range shot courtesy of Lucky Baloyi.
Balyoi ran onto a ball outside the area and his fierce volley had the beating of Wesley Fransman in the Stars goal, striking the post on the way in to make it 1-0 to Chiefs.
Kaizer Motaung Jr was menacing throughout, signalling his return to the Chiefs side after battling injuries.
Chiefs began the second period looking sluggish, seemingly content to sit on their slender one goal advantage.
Just after the hour mark, Chiefs should have doubled their lead.
Mandla Masango went on a bustling run down the right, before rounding the Stars keeper, but he waited too long to shoot and ended missing the target.
Later, the substitutes had their say on the match, as Chiefs free-wheeled to a 3-0 victory.
Nedbank Cup results on Saturday:
African Warriors 1 (Zakazaka 15) Jomo Cosmos 2 (Dondo 74, Nhlapo 90+1)
Golden Arrows 5 (Nkosi 2, Sheppard 41, Mbesuma 54, 76, Gabuza 79) North West Shining Stars 0
Kaizer Chiefs 3 (Baloyi 27, Khune 69, Majoro 71) Cape Town All Stars 0
Mpumalanga Black Aces 1 (Mweiikisa 42) Witbank Spurs 1 (Rooi 72) - aet
Spurs win 3-2 on penalties
Playing on Sunday:
Batau v SuperSport Utd, Powerlines v Mamelodi Sundowns
Played on Friday:
Maritzburg Utd 2 (Ncubeni 102, Sibisi 120+2) Bloemfontein Celtic 0 - aet