Vilakazi was widely expected to leave Wits after it was reported he had told his team-mates last week at training that it would be his last day at the club.
However, no deal was announced with some sources believing Vilakazi was stalling on signing with Sundowns in order to engineer a move to Chiefs instead, but the transfer has now been finalised.
While the fee was not disclosed, Wits revealed on their official website that Cuthbert Malajila and Mogakolodi Ngele would be joining them.
"Bidvest Wits FC are pleased to announce that they have reached agreement with Mamelodi Sundowns for the transfer of Sibusiso Vilakazi to Mamelodi Sundowns for an undisclosed transfer fee as well as the transfers of Cuthbert Malajila and Mogakolodi Ngele to Bidvest Wits FC," read the official statement.
"The players involved have all agreed personal terms with their respective new clubs and the transfers are, therefore, effective immediately.