On Monday magistrate Nishani Beharie transferred the matter to the high court.
"The magistrate's court lacks jurisdiction to determine the constitutionality of the legislation," Beharie said in her judgment.
Beharie said there were larger issues to be determined. A date is yet to be set for the matter to be heard in the high court.
Malema publicly accused Gordhan of being "corrupt", "a dog of white monopoly capital" and of hating black people.
Gordhan said the statements were intended to be hurtful, incite harm and promote hatred, and thus constituted hate speech, as contemplated by the act.
Gordhan is seeking an unconditional apology from Malema and Shivambu and R150,000 in damages.
He said, if successful, the damages claimed would be donated to a charitable organisation that supported job creation for unemployed youth.
At the time of lodging the complaint, Gordhan described Malema and Shivambu's utterances as "absolutely nonsensical" and unsubstantiated attacks.
"Enough is enough," Gordhan said.
"The determined defence of corruption and the corrupt using personal attacks, racism and alleged hate speech is not acceptable and must be challenged," Gordhan said in a statement after he had laid criminal charges.