Wits striker Phakamani Mahlambi opened the scoring with a penalty in the fifth minute after going down in the box under a challenge from Thamsanqa Mkhize.
However, defender Tshepo Gumede equalised in the 71st minute with his first topflight goal by nodding home a free-kick from Aubrey Ngoma at Cape Town Stadium.
In a contest of few chances, Mkhize threatened to score around the half-hour mark, but his header hit the side-netting following a delivery from City talisman Lebogang Manyama.
Soon after Judas Moseamedi failed to direct his header on target after a fumble left Wits goalkeeper Darren Keet stranded.
The result leaves Eric Tinkler's side on 46 points from 24 matches - a point ahead of Wits and Kaizer Chiefs, although the Students boast two games in hand.
Champions Mamelodi Sundowns are fourth with 44 points from 22 fixtures following a 1-0 win over SuperSport United on the same night.