The opening batsman has been named in the squad that will challenge world champions Australia in one-day matches in Melbourne on October 5, 7 and 9 in the inaugural Super Series.
Gibbs told News24 he hurt his right knee on South Africa's tour of the West Indies in April and subsequently aggravated the problem while playing for English club Lashings.
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"I have just told the manager Goolam Rajah (who is also the South African team's manager) that I won't be able to play.
"I have worked with the Western Province physio since my return from my Lashings duty but I am still feeling pain.
"I have also gone for an MRI scan where it showed that I had damaged the cartilage behind my right knee cap."
Gibbs was scheduled to see a specialist later on Thursday.
The other South Africans in the squad are all-rounders Jacques Kallis and Shaun Pollock and fast bowler Makhaya Ntini.
Pollock will captain the team.
