Spies had initially been given the all-clear after suffering the injury, to his left ring finger, during the Bulls' Super 15 final campaign last month.
But further scans since joining up with the Springboks revealed the problem - which is set to keep the 27-year-old, who has 50 Test caps - on the sidelines for up to three months.
"On review and further investigation, including a CT scan and assessment by a hand specialist in Cape Town, it was found that Pierre had a fracture into the joint," Springbok team doctor Craig Roberts said in a statement on the South Africa Rugby Union website.
"Surgical correction is needed in order to prevent permanent damage. The usual rehabilitation time for these kinds of injuries is eight to 12 weeks."
Spies' injury comes as a major blow to the Springboks who are already without injured forwards Schalk Burger, Juan Smith and Heinrich Brussow while Ryan Kankowski is unavailable due to club commitments in Japan.
Despite his injury worries South Africa coach Heyneke Meyer will not draft in a replacement for Spies ahead of their opener against new boys Argentina in Cape Town on Saturday.
"We have faith in the players in the squad and will consider the call-up of a possible replacement at a later stage," Meyer said.
"Losing Pierre is obviously a setback, because he is the most experienced member of our forward pack, but we will never take any risks with injured players.
"Injuries are part of the game and this now provides an opportunity for someone else to stake a claim."
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