Pekovic went to Charlotte where Dr. Robert Anderson performed a debridement and repair of the tendon. There is no timetable for his return but the Wolves are hopeful he will be healthy for training camp next season.
Pekovic played in just 31 games this season, averaging 12.5 points and 7.5 rebounds.
He is under contract for three more years and $36 million.
Pekovic has called this procedure his last best chance to relieve the pain in his foot.
The Wolves say Pekovic will be sidelined indefinitely.