Wits endured a disappointing 2017/18 campaign which saw them flirt with relegation.
Gavin Hunt side has now beefed up his squad as part of their preparations for the new term.
Macuphu caught the eye at the Chilli Boys after joining the club from National First Division (NFD) side Jomo Cosmos midway through the campaign.
The 29-year-old forward netted four goals in 13 matches for Chippa and the Clever Boys came calling for his signature.
Mzwakali also joined Chippa in January 2018 from Ajax Cape Town, but the speedy midfielder struggled for game time.
Despite making only four league appearances for the Eastern Cape side, the 24-year-old winger attracted interest from Wits, who have since snapped him up.
Mzwakali is seen as Vincent Pule's replacement with the winger having joined Pirates from Wits earlier this month.
The duo have reunited with Mhlongo at the Braamfontein-based club with the shot-stopper having spent the 2017/18 campaign on loan at Chippa from Pirates.
The 27-year-old keeper competed with Nigeria international Daniel Akpeyi for the Chilli Boys' number one spot and he could only make eight league appearances.
Pirates decided to sell Mhlongo to Wits at the end of the end of the season.
The lanky shot-stopper will fill the void left by Moeneeb Joseph, who is set to leave the Students for AmaZulu FC.
The Clever Boys made the announcement on their official Twitter page:
Bidvest Wits (@BidvestWits) June 22, 2018