Clever Boys attacker Kobamelo Kodisang, an off-season signing from Platinum Stars, forced a goal with an intended cross nine minutes into his debut after showing a good turn of pace in Bethlehem on Wednesday night.
However, Relebogile Mokhuoane equalised in the 34th minute for the hosts, who had defender Thamsanqa Teyise sent off in the 68th minute for a second bookable offence.
Rising talent Reeve Frosler looked to have scored a late winner for the visitors, but he then conceded a penalty at the death, which was converted by former Kaizer Chiefs hitman Mthembu.
Earlier Wits had a goal chalked off as Malawian forward Hellings Mahango was adjudged to have fouled his marker in the area.
The Students, who lost their Premiership opener 1-0 to Cape Town City, will revive hostilities with the Citizens in the MTN8 semi-finals in Cape Town on Sunday.
Coach Gavin Hunt and new signing Slavko Damjanovic will be back for the game after serving a two-match suspension following their dismissal in the MTN8 last-eight win over Golden Arrows.
Ea Lla Koto, who lost 1-0 to AmaZulu in the opening round of league fixtures, next entertain African champions Mamelodi Sundowns on September 13.