The 35-year-old will now work alongside Chiefs head coach Steve Komphela, who was in charge of Paintsil at Maritzburg United two seasons ago.
Paintsil's club career included stints with English sides West Ham and Fulham.
He replaces former South African international Doctor Khumalo as Chiefs' assistant.
Chiefs finished fifth in the 2015-2016 Premier Soccer League 25 points behind champions Mamelodi Sundowns.
The club, who won the title in 2015, also announced the signing of eight new players for the upcoming season including Zimbabweans, Edmore Chirambadare and Michelle Katsvairo from Chicken Inn.
One of the other players unveiled on Monday was Sundowns captain and defender Ramahlwe Mphhahlele, who made his international debut for Bafana Bafana in their 4-0 Africa Cup of Nations qualifier win over Gambia earlier this month.
The Chiefs however will be without Togo international striker Camaldine Abraw for nine months with an unspecified injury.
As well as Paintsil there were two more additions to the coaching staff  with Brazilian Alexandre Revoredo as the new goalkeeping coach and his compatriot Marco Munhoz as physical trainer.
Former South Africa international Brian Baloyi remains with the club as part of the goalkeeping department.
Former Ghana international defender John Paintsil has been appointed as the new assistant coach of South African Premier League club Kaizer Chiefs.