According to a source close to Wits, the move forms part of the deal that saw goalkeeper Brighton Mhlongo join the Clever Boys, which was announced this morning.
Motshwari, however, must still finalise personal terms with the Sea Robbers.
"Both Wits and Pirates have agreed on the deal," says the informant.
"Everything now is between the player and Pirates in terms of personal terms."
The 27-year-old struggled for game-time in 2017/18, only making 11 appearances for Gavin Hunt's side as the Students finished outside of the top eight after winning their maiden league title the season before.
Wits have also been linked with a move for Buccaneers striker Thamsanqa Gabuza, while Pirates earlier confirmed the sale of winger Riyaad Norodien to Cape Town City.