City chairman John Comitis made the announcement at a press conference held on Tuesday, confirming that McCarthy has signed a three-year deal.
Following the departure of Eric Tinkler to SuperSport United the Citizens moved quickly to secure a new man for the role of head coach.
Switftly installing McCarthy as head coach gives the former Bafana Bafana hitman an opportunity to thoroughly prepare for the upcoming 2017/18 campaign.
As well as being the national team's all-time leading goalscorer, the 39-year-old enjoyed a lengthy career overseas playing for European heavyweights Ajax Amsterdam and FC Porto as well as English outfit Blackburn Rovers.
McCarthy has a UEFA A coaching license and has previously spent time in the dugout as an assistant coach with the Belgian outfit Sint-Truiden VV.