A brace from Bernard Parker and a goal from Mulomowandau Mathoho handed the Amakhosi their 10th League win of the season which sees them sit 11 points clear at the top of the table.
Wits' fifth loss of the season sees them drop to sixth place with 20 points.
Parker opened the scoring in the 21st minute after latching onto a knock-on header from Kingston Nkhatha, despite suspicions of handball, and then proceeding to fire past Moeneeb Josephs from 14-yards out on the left side of the small box, 1-0.
The home side, though, nearly hit back seven minutes later when Sameehg Doutie saw his volley from just outside the box strike the left post before going out of play.
Chiefs doubled their lead in the 37th minute after Mathoho headed home a pin-point free-kick from Siphiwe Tshabalala to take them into the break at 2-0.
Wits dominated the second half with almost 70 percent of the possession, but they could not break down a resolute Chiefs defence.
Instead, against the run of play, the Amakhosi put the match to bed with their third goal in the 70th minute.
It was some great build-up play for Chiefs that led to the goal when George Maluleke played Parker through on goal and he calmly chipped the ball over an onrushing Josephs to make it 3-0 and wrap up the tie.