The flanker has a pinched nerve in his neck, which he suffered in the 14-10 defeat by the All Blacks in Wellington, and is likely to be out for two months after consulting doctors on Tuesday (local time).
He joins team mate Ruan Pienaar, who is out for six weeks with a knee ligament tear, on the injury list.
"This is another setback as we prepare to host Australia and New Zealand in two very important matches as Francois has been superb for us in the last couple of seasons," Springbok coach Heyneke Meyer said in a statement on Tuesday.
Experienced back JP Pietersen was called up to replace Pienaar but Meyer said a replacement for Louw would only be named later this week.
South Africa host Australia in Cape Town on September 27 and then play the All Blacks again in Johannesburg on October 4 in their last two matches of the annual four-nation southern hemisphere championship.
