He faces a lay off of up to eight weeks after a medial collateral ligament injury playing for the Stormers in Saturday's Super Rugby loss to hosts Waratahs in Sydney, a Stormers statement said on Monday.
Vermeulen suffered similar serious knee injuries at the same stage of the last two seasons.
The 26-year-old, with seven caps since his debut last September, misses out on next month's three tests, which are against Italy, Scotland and one of the two teams or Samoa on three successive Saturdays from June 8 to 22.
South Africa are already without flanker Schalk Burger and backs Johan Goosen and Francois Steyn for the home series.
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