Last week, Madonsela told Eyewitness News she was willing to risk being painted as supporting the party because her powers should not be defined without her being represented.
The public protector will now join the case as a respondent in the matter.
In her report, she recommended the president pay back a portion of the money spent on non-security upgrades at his Nkandla homestead in KwaZulu-Natal.
The public protector's spokesperson Kgalalelo Masibi says Madonsela now has until the end of the month to file court papers.
“The public protector welcomes the decision of the Constitutional Court and she thinks it’s a good decision because she will in a position to shed light on the powers of the public protector.”