Last week, Pienaar, who is 35, officially became a free agent after his contract with English club Sunderland AFC came to an end.
The former Ajax Cape Town midfielder was linked with his childhood team, Pirates and their rivals Chiefs.
Pienaar, who was also linked with Cape Town City, held informal talks with Pirates last year before he joined Sunderland on a one-year deal.
On Wednesday, Wits revealed that they had signed Pienaar on their official Twitter account.
Bidvest Wits (@BidvestWits) July 5, 2017
The Clever Boys also completed the signing of Montenegrin defender Slavko Damjanovic.
The player has been signed as cover for Buhle Mkhwanazi, who is out nursing a long-term injury.