The ex-AmaZulu and Golden Arrows mentor has penned a one-year deal with the Chilli Boys, with an option to extend.
Roger Sikhakhane, who led the Cape side to promotion, will be retained in another capacity.
"I am excited about the prospect," Mngqithi was quoted as saying by the Cape Times.
"I also did my homework on the club and so far everything is going well. We will be aiming very high in the season."
Mngqithi, an MTN8 winner with Arrows in 2010, was fired by Usuthu early last term.
The former school teacher went on to assist Shakes Mashaba with the South Africa U-23 team in an Olympic qualifying tournament in Morocco in December 2011.
United general manager Wanda Mbenguzana is confident Mngqithi will prove an asset.
He said: "When we made the decision, along with the chairperson (Chippa Mpengesi), we decided that his experience and history of working with the youth will assist us.
"Manqoba is very familiar with this, considering that we have a lot of young and inexperienced players at the club."