The South African damaged his left knee on a sailing holiday last week and had an operation yesterday.
The injury means he will miss the USPGA Championship at Baltusrol next month and the Presidents Cup in September.
He has withdrawn from the Tour schedule and it is unclear when he will return.
PGA Tour commissioner Tim Finchem said: "Our best wishes go to Ernie for a speedy recovery following his recent knee surgery.
"His presence will be missed at the remainder of this year's PGA Tour events and during the upcoming Presidents Cup.
"We all know what a tough competitor he is and are confident he will rejoin the Tour as soon as he can."
The 35-year-old, nicknamed the 'Big Easy', won back back-to-back European Tour events in Dubai and Qatar in March but has otherwise endured a frustrating year.
He failed to make an impact any of the first three majors, finishing 47th at the Masters, 15th at the US Open and 34th at the Open.Reuse content