Pienaar injured his medial cruciate knee ligament on Saturday as the Springboks went down 14-10 to New Zealand in Wellington and is ruled out for the rest of the competition.
The 28-year-oLd Pietersen, who has 54 caps, was not available for selection for South Africa's first four matches of the tournament.
"JP has always been part of our plans and did very well in June playing at outside centre," said Springbok coach Heyneke Meyer.
"We've got two scrum halves in the squad in Francois Hougaard and Cobus Reinach and decided it would be better to bring in an outside back such as JP, who covers wing and outside centre."
The 30-year-old Pienaar, who plays for Ulster, will go for scans on Monday after which the exact extent of the injury will be determined, SARU added.
South Africa host Australia in Cape Town on Sept. 27 and then play the All Blacks again in Johannesburg on Oct. 4
