The match will now be played in Lahore at the Gaddafi Stadium on the same date of October 29, Shafqat Naghmi, PCB chief operating officer said.
"The match has been shifted to Lahore over security fears raised by South Africa," Naghmi told AFP.
South African team security were not convinced by top-level officials in Karachi during a meeting about player safety in the port city on Wednesday morning, officials said.
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"We deeply regret this decision especially for the people of Karachi for having deprived them of this opportunity... "
Logan Naidoo, South Africa team manager |
"We are disappointed and feel that Karachi is safe to hold any international event but we had no choice but to accept the decision of the South African management," Naghmi said.
Logan Naidoo, South African team manager, said his squad regretted that the decision had to be taken.
"We deeply regret this decision especially for the people of Karachi for having deprived them of this opportunity but unfortunately the members of the South Africa contingent were not comfortable in travelling to Karachi," Naidoo said in a statement.
He added that the decision was reached after consultation with officials back in South Africa.
History of violence
South Africa held meetings with Pakistan officials in the wake of the suicide attack and had been assured of increased security for players, prompting them not to end the tour prematurely last week.
Karachi has been a danger zone for international teams given the city's history of extremist and ethnic violence, and South Africa refused to play there on their last tour four years ago.
New Zealand cut short a tour after a bomb blast outside their hotel killed 14 people, including 11 French naval staff, in May 2002.
Karachi was cleared for international cricket only when India played a five-day Test there last year.