The Clever Boys welcomed an in-form Maritzburg United side which had won its last three games in all competitions at the Bidvest Stadium in Johannesburg.
The hosts broke the deadlock through Keegan Ritchie, who hit the back of the net with a thunderous shot from a free-kick to make it 1-0 to Wits in the 15th minute.
The Team of Choice tried to level matters, but they could not beat Wits goalkeeper Darren Keet, who had a relatively quiet first half.
The score was 1-0 to Wits at the break with the hosts having dominated the first half.
Maritzburg came back rejuvenated after restart following a half-time team talk with their coach Fadlu Davids.
Second half substitute Mohau Mokate made an immediate impact as he beat South Africa international Darren Keet to make it 1-1 in the 78th minute.
However, Buhle Mkhwanazi proved to be the hero for Wits as he scored with a header from a well-taken corner-kick with six minutes left to make it 2-1.
The match ended 2-1 in favour of Wits, who moved up to eighth on the PSL standings, while Maritzburg remained third on the table.
The score was 0-0 at the interval with the two teams having created goalscoring opportunities without convert ing them.
The deadlock was finally broken five minutes into the second half, and it was Mhlengi Cele, who beat Ajax keeper Jody February to make it 1-0 to AmaZulu.
However, the lead only lasted for 10 minutes as Rodrick Kabwe scored with a beautiful free-kick to make it 1-1, silencing AmaZulu fans out in the stands.
Both teams searched for a late winner, but it was Siyanda Zwane who netted an own goal to hand the home side a 2-1 win on the night.
The victory took AmaZulu to ninth place on the PSL standings, while Ajax remained 15th on the table.