Burger has not played since he tore medial ligaments while captaining the Stormers on the opening weekend of the Super 15 season in February.
The 29-year-old's had hoped to return for the opening Test on June 9 but, after missing the Stormers' recently-completed four-week tour, the club today admitted they did not expect him to recover in time.
"Schalk Burger, Duane Vermeulen and Nick Koster (all knee injuries) are expected to return only after the June break," a statement on the club's website read.
Vermeulen's exclusion also comes as a blow to the Springboks after the number eight enjoyed a good start to the season before also succumbing to a knee injury.
Burger was at the centre of controversy three years ago when he was banned for eight weeks after he was found guilty of eye gouging British and Irish Lions winger Luke Fitzgerald.
Gilbert has released a new line of rugby cleats. The Gilbert Virtuo 8S is part of the exciting new product. Check it out.
The entire All Blacks apparel line has been updated for 2013/14. Check out the New Zealand All Blacks polo.
The Nike Tiempo is a solid rugby cleat and one of few styles still made from full-grain natural leather.
The Gilbert Blitz 8S rugby cleat is a great cleat at a great price of $69.99. Get a new pair of cleats today.
A cool looking all black rugby cleat with the high performance adidas is known for. Get in the Gear!
Wear the crest of the British and Irish Lions on your t-shirt. A great look for the summer.
The All Blacks Performance t-shirt is black with hints of blue from the training jersey. Very Cool.
The New Zealand All Blacks training jersey for 2013/14. Get in the Gear!
The USA Rugby Pro Alternate rugby jersey is perfect for any fan of the Eagles. Get yours to wear during the summer Test matches.
The NEW All Blacks 2013/14 jersey has arrived at World Rugby Shop. Dare to wear the colors of the All Blacks.