South Africa will play a Test and a warm-up match in the southwestern Pakistani city of Karachi, a venue where they refused to play over security fears four years ago.
The itinerary for their tour announced by the Pakistan Cricket Board (PCB) includes two Tests, a three-day match and five one-day internationals.
Foreign teams have refused to play in Karachi, which has been troubled by violence, in the aftermath of the September 11 attacks and over fears about security in the region.
"The South Africans showe no reservations in playing in Karachi and approved the city as the venue for a warm-up match and for a Test," PCB chief operating officer Shafqat Naghmi said.
More than 40 people were killed in Karachi last month in some of Pakistan's worst political violence.
The Proteas are also scheduled to play a one-day international at the border city of Peshawar, where teams have refused to play due to its close proximity to Afghanistan.
Pakistan had to play their home series against Australia and the West Indies at neutral venues in 2001 and 2002 as both teams refused to tour the country over security fears.
New Zealand agreed to tour in 2002 but were forced to cut it short after a bomb blast near their hotel killed 14 people, including French naval staff. South Africa then refused play any match in Karachi on their tour in 2003.
The Proteas will arrive in the last week of Sepember and open the Test series with the first Test in Karachi from October 1.