The powerful second row was due to team up with Top 14 outfit Toulon at the end of the tournament.
However his move to France could come sooner than Botha would have hoped for after he suffered a recurrence of an Achilles injury in training.
Botha had missed the encounters with Wales and Samoa with problem but he had hoped to return to action against Australia in the last-eight showdown.
The 32-year-old will now return home to seek treatment advice from a specialist, though, after landing badly during a lineout on Wednesday.
"I'm very disappointed after all the hard work that has been put in over the past few months, but it's not about me, it's about the team now and there's still a big job to do," Botha said.
"I'll be sitting at home with my family on Sunday with a tear on my cheek as the team takes on the Wallabies.
"But we can't stop here - there are still three games left to play."
Despite the injury and his move to France, Botha insists he still has ambitions to play for the Boks again.
"This is definitely not the end of my Test career as far as I am concerned," he said.
"I'll be aiming to give 100 per cent to Toulon to help them get into the European Cup and I'll still be available for South Africa next year.
"I still have the desire to play for my country and that will be there for as long as I play. It's a special thing to pull on this jersey and that hunger has not left me."
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