Maharaj suffered the injury while scoring 51 in the second innings with the Proteas eventually going on to win the Test by 328 runs.
The left-arm spinner went past the 200-wicket milestone in Bulawayo, the first Proteas spinner achieve the landmark in Test cricket.
Senuran Muthusamy has been named as a replacement in the squad while Prenelan Subrayen was already with the team in Zimbabwe and could make his Test debut if selected.
Proteas head coach Shukri Conrad said: "This is part of Wiaan's journey where he is starting to take more responsibility in the side.
"He has captained in his youth days, I think it was for the South Africa U-19s.
"I think it will be a great opportunity for Wiaan to grow into becoming a leader in this group. He has got all the attributes and the more responsibilities I give him the better he reacts."
Other news from the Proteas camp is that fast bowler Lungi Ngidi, who was to join the squad ahead of the second Test, has been released to give the seamers who impressed in the first Test another opportunity to build on their performances.
The second and final Test of the series starts at the Queen's Sports Club in Bulawayo on Saturday.
Corbin Bosch admits he has not yet come to grips with matching the feat of legendary Proteas all-rounder Jacques Kallis in the first Test victory against Zimbabwe in Bulawayo.
Corbin Bosch picked up a maiden five-wicket haul as the Proteas wrapped up a mammoth 328-run victory in the second session of the fourth day of the first Test against Zimbabwe in Bulawayo.
Wiaan Mulder hit a career-best 147 as the Proteas were bowled out for 369 in the second innings to set Zimbabwe a mammoth target of 537 with two days remaining of the first Test in Bulawayo.
Lhuan-dre Pretorius became the youngest player to score a Test century for the Proteas to help the visitors recover from 55-4 to post 418-9 at stumps on day one against Zimbabwe in Bulawayo.
