Morocco is in the same group (Group K) as Bafana Bafana along with Zimbabwe and Liberia with qualifiers starting at the end of this month.
"We understand the challenges of stadia on the continent, but we plead that it not be used to disadvantage other countries or give an unfair advantage to others," reads part of the letter from SAFA addressed to CAF.
The Lone Stars have opted to stage their home games at the Grand Stade de Tanger in the Moroccan port city of Tangier as the Samuel Kanyon Doe Sports Complex in Monrovia doesn't meet the required CAF standards.
They have already played their last two games in Morocco against Nigeria and Central Africa Republic in Morocco in qualifiers for this year's World Cup after having also played against Cape Verde in Ghana.
The latest developments mean Morocco will only play two away games in the group after having played all six in their group for World Cup qualifiers at home with Guinea-Bissau and Sudan faced with the same situation as Liberia while political instability in Guinea forced them to also play away from home.
Tangier is preferred due to its proximity to Europe a sizeable portion of the Liberian squad play.
Last year Ethiopia opted to play their 2022 World Cup qualifiers home game against Ghana in South Africa despite Bafana Bafana being in the same group.
Just like SAFA has done now, Ghana complained but the match still went on at Orlando Stadium.
The GFA felt that their game against Ethiopia shouldn't have been played in a country which is in the same group for fairness purposes, the same issue that SAFA is now raising in Liberia playing their home games in Morocco.
Sao Tome and Principe also opted to play their 2021 AFCON qualifiers home game against Bafana Bafana in Port Elizabeth in November 2020 giving South Africa the benefit of playing four of their six games at home.
Bafana still failed to finish among the top two teams in the group which also featured Ghana and Sudan.
Namibia and Malawi have also played their home games in South Africa in recent times due to matters relating to stadiums in their respective countries not meeting CAF requirements.