Ashraf Hendricks scored for the Students, while both teams ended the match with 10 men after BidVest Wits’ Phil Evans and Cosmos’ Bamuza Sono were both sent off in the second half.
The visitors threatened Moeneeb Josephs’ goal in the fourth minute when Davies Mwape forced the Bafana Bafana keeper into producing a good save to deny the striker’s low shot from hitting the back of the net.
Mwape should have opened the scoring three minutes later when he ran through the Students’ defence, but with just Josephs to beat, the Zambian sent his effort wide.
The Clever Boys wasted a glorious opportunity in the 13th minute when Calvin Sosibo was played through on goal by David Radebe, but the midfielder shot tamely at Avril Phali.
The match remained goalless at the break.
The hosts threatened two minutes after the restart when they were awarded a free-kick on the edge of the Cosmos area, but Phali produced a good save to deny Phil Evans.
Cosmos took the lead in the 67th minute when Laffor opened the scoring with a header from a cross by Dikgang Mabalane, but the goal was marred by the sending off of both Evans and Sono, who were involved in an of-the-ball incident as the Ezenkosi players were still celebrating their goal.
Phali produced another superb save three minutes from the end when he denied his opposite number, Josephs, from hitting the back of the net with a header from Almiro Lobo’s free-kick.
However, there was not much the Cosmos keeper could do when Hendricks headed home from a corner a minute later.
But the Ezenkosi netted the winner in the dying second when Laffor produced a spectacular scissors-kick to beat Josephs and hand Cosmos a deserved win.