Chief Justice Mogoeng Mogoeng read out the judgment on Thursday saying Mbete was wrong when she claimed she did not have the powers to allow for a secret ballot vote.
He said the Constitutional Court did not have the power to order the speaker to make such a decision.
Mogoeng set out some avenues on what Mbete should consider when weighing whether or to allow such a vote.
Mbete had argued that she had no issue with a secret vote, but she had no powers to do so.
The case was brought by the UDM, EFF, COPE and civil society organizations in May.
The UDM argued that ANC MPs would be intimidated and faced party pressure if the vote was not done in secret.
Political parties react to ConCourt judgement on #SecretBallot. They are all pleased. @IOL pic.twitter.com/1OdV7eZ6I1
— Zintle (@ZintleMahlati) June 22, 2017
Mogoeng says it's up to National Assembly, through speaker, to allow for a open vote or a Secret Ballot in no confidence vote.
Mogoeng in his ruling said MPs were not bound to their parties and were instead there to serve the public as elected officials. Mbete would have to ensure that MPs are protected.