Phakaaathi had reported that Mhango was unhappy at Wits and was looking for a move away from the club.
Mhango told reporters during the Cosafa Cup tournament that he had agreed on a new one-year deal and would be staying at Wits after his deal expired and he was linked with a move to Chiefs as a free agent.
The 26-year-old was a key player in Gavin Hunt’s set up when the club won their first league title.
Pirates and Wits have reached an agreement to the player to move from the Clever Boys to the Sea Robbers.
Mhango is expected to undergo medicals on Thursday at the club before he joins his Pirates teammates for his first training session in the afternoon.
“Orlando Pirates Football Club would like to thank Wits’ management for the professional manner that these negotiations were conducted,” read a statement from Pirates.
Bafana Bafana midfielder Ayanda Patosi is expected to join Pirates from Cape Town City soon.
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