They are joined on the injury list by centre Jean de Villiers and his fellow back Butch James as the Springboks look to build from their 17-16 victory over Wales last weekend.
Lock Matfield has a hamstring injury, although there is some good news for South Africa with the return of his regular second-row partner Bakkies Botha after an Achilles problem.
Wing Habana has a leg injury, while De Villiers (rib cartilage) and James (hip) also miss out, with substitute lock Johann Muller facing a late fitness test on his hamstring.
Botha replaces Matfield in the starting line-up, Odwa Ndungane takes over from Habana and Frans Steyn moves from full-back to replace de Villiers, with Pat Lambie wearing the number 15 shirt.
"We have had injury problems at lock, but we have versatile players to cover for most situations," said Springboks coach Peter de Villiers.
"Danie Rossouw has now been picked to start at four, five, seven and eight this season, and he will call the lineouts this weekend.
"Against a tough proposition like Fiji you would prefer to have all your players available, but this is tournament rugby and we picked our squad knowing that we would have to cover for many situations."
Team: P Lambie; J P Pietersen, J Fourie, F Steyn, O Ndungane; M Steyn, F du Preez; G Steenkamp, J Smit (captain), J du Plessis, B Botha, D Rossouw, H Brussow, S Burger, P Spies.
Replacements: B du Plessis, T Mtawarira, J Muller, W Alberts, F Hougaard, R Pienaar, J de Jongh.
Gilbert has released a new line of rugby cleats. The Gilbert Virtuo 8S is part of the exciting new product. Check it out.
The Barbarians are one of the top invitational rugby sides with a long history and classic rugby jersey.
The Nike Tiempo is a solid rugby cleat and one of few styles still made from full-grain natural leather.
The Lions get ready for their matches with this green training jersey. It's what the players wear. Get in the Gear!
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 Lions are ready to get their Australia tour underway. They arrive in Perth on Monday.
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.