This comes after a complaint was lodged over the overall performance of Ghanaian referee Joseph Lamptey on the day.
The Court of Arbitration for Sport (CAS) upheld the lifetime ban of Lamptey, meaning Bafana Bafana's 2-1 win over Senegal has been chalked off with immediate effect.
Below is a statement released by Fifa on Wednesday night.
"The Bureau for the FIFA World Cup Qualifiers ordered a replay of the qualification match between South Africa and Senegal held on 12 November 2016."
“The Bureau for the FIFA World Cup Qualifiers ordered a replay of the qualification match between South Africa and Senegal held on 12 November 2016,” Fifa said in a statement late on Wednesday night.
“This decision follows the confirmation of the Court of Arbitration for Sport (CAS) to uphold the lifetime ban of match referee, Joseph Lamptey, for match manipulation, the ruling imposed by the Fifa Disciplinary and Appeal Committees.
“The match will be replayed within the November 2017 international window, with the exact date to be confirmed in due course.
“As stated in the Fifa World Cup regulations, this decision shall come into effect immediately, but shall be subject to confirmation by the Organising Committee for Fifa Competitions at its next meeting, scheduled for 14 September.”
These latest developments mean South Africa now have a single point in Group D, and will have to win fairly to reclaim the four points they already had in the bag.
Meanwhile, the South African Football Association (Safa) has denied all wrongdoing, and vowed to study Fifa's report before deciding whether or not to appeal the decision.
"SAFA is studying the contents of the report and will issue a statement on intentions to challenge that decision. SAFA wishes to also state categorically that it was in no way involved with any wrongdoing related to the actions of the referee, as stated in the FIFA report," Safa said in a statement.