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He appeared before magistrate Alfreda Lewis, who transferred the matter to the Specialised Commercial Crime Court in Bellville, where he is to make his first appearance on October 31.
Malgas, 26, faces charges of perjury and corruption.
Malgas has to report to police on Tuesdays and Fridays, as bail conditions, and was ordered to surrender his passport to the police official investigating his case.
He was banned from making any contact with listed State witnesses.
The magistrate warned him: "If you know any of the witnesses, you may not make contact with them, directly or indirectly."
Malgas told the court he had appointed a privately funded attorney, who was not at the proceedings.
It later transpired that his lawyer had not left Johannesburg yet.
The magistrate warned Malgas to ensure his lawyer was present when he appeared in the commercial court.
Malgas was arrested last Thursday at the school in Eldorado Park, Johannesburg, where he works as an administrator, and first appeared in the Protea Magistrate's Court before his transfer, in custody, to Cape Town.
He allegedly "fixed" soccer matches in the Vodacom Tournament in June 2011.
Earlier this year, former Bafana Bafana assistant coach Phil Setshedi, 57, was jailed for eight years for paying a police official, posing as the chief referee, R2 000 to manipulate the outcome of soccer matches in the tournament.
Setshedi was arrested on June 8, 2011, after SAFA reported him to the police following representations to officials, in an alleged attempt to influence the outcome of a match.
He had travelled to Cape Town to bribe the referee to ensure the Mpumalanga Sevutsa Stars won two matches.
Malgas was one of three witnesses to testify against Setshedi. It is alleged Malgas lied to the court under oath, which forms the basis for the perjury charge.
After Setshedi's prosecution, Malgas and the two other referees who testified were suspended from the sport.
On the corruption charges, Malgas allegedly manipulated the outcome of a match during the 2011 second division play-offs in Cape Town.
