Du Plessis injured his right knee early in the Springboks' 27-6 win over the Pumas in Cape Town on August 18.
He was taken for scans during the game, which confirmed the diagnosis of an injury to his medial and anterior cruciate ligaments.
Du Plessis requires surgery and he will be out for the remainder of the season.
Apart from Du Plessis, the match day 22 have been retained and five players added to provide depth - Tiaan Liebenberg and Burden (hookers), Dean Greyling (prop), Juandré Kruger (lock) and Jano Vermaak (scrum-half).
Following the Springboks' return from Argentina, the national selectors will meet to select a touring squad of 28 that will travel to Australia and New Zealand for the third and fourth rounds of the Rugby Championship.
"We only finalised the touring squad after the Test against Argentina at Newlands on Saturday afternoon as we wanted to first assess the injury situation," said Springboks coach Heyneke Meyer. "It's never nice to leave behind players, but we're only permitted to travel with 26 players.
"The players that stay behind will benefit from game time in the Absa Currie Cup and will certainly be in the selection frame when we select the squad for the next leg of the Rugby Championship."
South Africa squad:Forwards: Willem Alberts, Andries Bekker, Craig Burden, Pat Cilliers, Marcell Coetzee, Keegan Daniel, Jannie du Plessis, Eben Etzebeth, Dean Greyling, Juandré Kruger, Tiaan Liebenberg, Tendai Mtawarira, Jacques Potgieter, Adriaan Strauss, Flip van der Merwe.
Backs: Jean de Villiers (captain), JJ Engelbrecht, Bryan Habana, Francois Hougaard, Zane Kirchner, Patrick Lambie, Lwazi Mvovo, Ruan Pienaar, Frans Steyn, Morné Steyn, Jano Vermaak
Gilbert has released a new line of rugby cleats. The Gilbert Virtuo 8S is part of the exciting new product. Check it out.
The entire All Blacks apparel line has been updated for 2013/14. Check out the New Zealand All Blacks polo.
The Nike Tiempo is a solid rugby cleat and one of few styles still made from full-grain natural leather.
The Gilbert Blitz 8S rugby cleat is a great cleat at a great price of $69.99. Get a new pair of cleats today.
A cool looking all black rugby cleat with the high performance adidas is known for. Get in the Gear!
Wear the crest of the British and Irish Lions on your t-shirt. A great look for the summer.
The All Blacks Performance t-shirt is black with hints of blue from the training jersey. Very Cool.
The New Zealand All Blacks training jersey for 2013/14. Get in the Gear!
The USA Rugby Pro Alternate rugby jersey is perfect for any fan of the Eagles. Get yours to wear during the summer Test matches.
The NEW All Blacks 2013/14 jersey has arrived at World Rugby Shop. Dare to wear the colors of the All Blacks.