Lebogang Manyama bagged a brace in a seven-goal thriller that saw Wits come from behind twice, with goals on either end in quick succession.
Wits threatened early on as Siboniso Gaxa flashed a ball across the face of the City goal, but none of his teammates were alert to get onto the end of it.
However, three minutes later Roland Putsche had the visitors in front with a well-taken low shot into the bottom corner, after Wits failed to clear their lines from an Aubrey Ngoma cross.
The home side pushed for the equaliser and pegged the Cape-based side back into their own half, and came close when Rodgers headed narrowly over the crossbar midway through the half.
Though, the pressure finally paid off just past the half-hour mark, when Bongani Khumalo cleverly got onto the end of a Elias Pelembe corner to head home the equaliser for the hosts.
The pace of the game steadied as neither outfit were willing to open up to concede before the half-time break, as they went into the tunnel at 1-1.
Two quick goals on either side close to the hour mark saw CT City take the lead before Wits grabbed an equaliser after two goalkeeping errors.
Darren Keet rushed off his line to clear a ball over the top, but scuffed his clearance allowing Manyama to tap into an empty net in the 57th minute.
However, Walters on the other end was adjudged to have brought down Mogakolodi Ngele inside his area, with Eleazar Rodgers slotting the penalty home in the 59th minute.
Despite bossing proceedings for most of the second half, Wits were unable to turn their dominance into goals as they scuffed numerous opportunities.
They were eventually made to pay as captain Manyama sealed his side's victory with a header in the final minute of stoppage time.
The win sees the Clever Boys suffere their second succesive defeat in the league, while City extend their lead to four points, while second-placed SuperSport United have a game in hand.