The 52-year-old, who has been working as a television pundit and part-time coach, is expected to develop young talent and create a uniform playing style for national teams.
National football association official Natasha Tsichlas said: “Neil understands the South African football culture and has a successful track record.”
Tovey skippered Bafana Bafana to a 2-0 triumph over Tunisia in the 1996 Cup of Nations final in Soweto, watched by a capacity 80,000 crowd that included then President Nelson Mandela.
His 52-cap international career ended a year later after a poor performance in a World Cup qualifying defeat away to Congo in Brazzaville.
Pretoria-born Tovey spent 10 years playing for Kaizer Chiefs, the most popular and successful football club in the republic.
The highlight of his coaching career was guiding Mamelodi Sundowns to the South African Premiership title.