The 28-year-old buckled in pain after only six minutes of his side's home defeat against promotion rivals Millwall and was carried off on a stretcher.
Leeds manager Simon Grayson said: "I am absolutely gutted for the lad. Paddy's dream was to play in the World Cup and it looks like that dream has been shattered.
"Unfortunately he picked up a severe Achilles injury which will rule him out for the rest of the season and probably the World Cup as well. It is a huge blow for Paddy who has been a real warrior for us this season."
Kisnorbo, who has 18 caps for his country, had been expected to be named in Pim Verbeek's Socceroos squad for South Africa.