The operation was performed by Dr. Sanjay Jantana.
Fernandez is expected to miss the remainder of the regular season but might be back for the playoffs.
He missed a dozen games with a lower back strain, which flared up against Dallas on March 19, prompting further evaluation.
Fernandez was acquired by the Nuggets along with Corey Brewer in exchange for a future second-round draft pick last December. He averaged 8.6 points, 2.1 rebounds, 2.4 assists and 1.03 steals in 31 games for Denver.