Australia are due to play four one-day internationals against Zimbabwe and South Africa, starting in late August.
However, Coulter-Nile, who was a member of Australia's ICC World Twenty20 squad, will play no part after he suffered a recurrence of the issue that blighted his participation in the Indian Premier League with the Delhi Daredevils.
"Nathan has had a recurring left hamstring tendon injury over the past four months and required surgery to repair the damaged tendon to give it the best chance of recovery," said Australia team physiotherapist Alex Kountouris.
"Nathan will now commence a rehabilitation program, however he is unlikely to be bowling again in time to be available for the ODI tri series in Zimbabwe.
"We will take our time with Nathan's recovery to ensure he is fully fit for the big summer of cricket ahead."
Coulter-Nile joins David Warner in being absent from the tour following the batsman's decision to stay in Australia ahead of the birth of his first child.