The appointment of Petersen will help the association to drive its vision for a new strategic direction to deliver on competitive national teams for both men and women; strong focus on development at grassroots level.
He will also help the association to enhance the international profile of South African football, ensuring that the commercial programme of the association delivers the resources to achieve these objectives.
The search for a suitable person was a long and intense process. The panel responsible for the search finalised the process and their recommendation was accepted by the Management Committee of Safa on Tuesday.
Safa President Kirsten Nematandani said: We would like to thank all the candidates for offering to serve South African football.
We believe that Dr Petersen has the necessary qualifications, experience and expertise in business and football to assist Safa to deliver on the mandate outlined earlier in this statement.
"We are happy to have made this appointment and now we can focus on our core business of running the game of football in this country."
Nematandani said the reason they took so long to find a new CEO was that they were not finding a suitable candidate.
Petersen was CEO of the Premier Soccer League (PSL) between 2000 and 2001 when he left football to be involved in business.
"I am excited, and humbled by this appointment. I look forward to the challenges, to working with the team at Safa to ensure we take the association to greater levels. I am passionate about the game of football, and I could not stay away from it for too long. I am also passionate about football development and will strive to ensure we work hard on it. To ensure our success, we need to ensure we put the right structures administratively, commercially and strategically," said the new Safa CEO.
Lehoko said: I believe this is the best appointment and will work for the betterment of the game. I have worked with him before during South Africa's 2006 FIFA World Cup bid.
I know he can deliver because he has the passion for the game, and he will get all the support he needs. I would like to thank the association for believing in me and allowing me the opportunity to lead this organisation, I have learnt a lot from this experience.
"I would also like to thank my colleagues for helping me through this period, as well as the media for the support."