Siphiwe Tshabalala got a brace; Stembiso Ngcobo and George Lebese made it four.
After playing to an exciting 1-1 draw in the League midweek, a lot was expected from both teams in their Nedbank Cup clash, but despite the four goals the match failed to produce similar excitement.
Chiefs were the dominant side as the Clever Boys struggled to keep up with, with Siphiwe Tshabalala calling the shots and giving the home side all sorts of trouble.
Amakhosi made their intentions clear in the first few minutes, and Darren Keet produced a great save to deny Siphiwe Tshabalala.
However there was nothing to stop 'Shaba' three minutes later as he beat the offside trap before rounding off the goalkeeper to put his side ahead.
Wits striker Sifiso Vilakazi had a header miss the target in the 16th minute.
In the 33rd minute, Amakhosi doubled the lead when Sthembiso 'Mapholoba' Ngcobo tabbed in a corner-kick from Tshabalala.
The score at half-time was 2-0.
In the 47 minute, Sibusiso 'General' Vilakazi played a neat one-two with Stanton Fredericks but Vilakazi's shot narrowly missed the target.
Tshabalala should have increased Chiefs' lead in the 73rd minute but sent his close range shot wide.
Two minutes later Shaba made up for his earlier miss as he beat two defenders before completing his brace.
In the 80th minute, Tshabalala was replaced by George Lebese, and within three minutes of being on the pitch Lebese grabbed the fourth goal for Chiefs, netting with a spectacular long-range free kick that beat Keet hands down.
In the last minute of the match, Sifiso Myeni was given his marching orders, a decision that left everyone puzzled.