Harris, 34, bowled Michael Clarke's men to a thrilling series victory over South Africa on away soil earlier in March, heroically taking the final two wickets in the space of three balls to win the deciding Test in Cape Town.
The Queenslander's knee issue was the world's worst kept secret, and Australia confirmed Harris had surgery on Tuesday.
"Ryan underwent surgery yesterday on his right knee, which included a clean out of some loose bits of bone and removing bone spurs within the joint," team physio Alex Kountouris said in a release.
"Ryan will be on crutches for a few weeks and we expect a long rehabilitation period. Hopefully for Ryan he will be fit to play in the Test series against Pakistan later in the year but we will continue to assess his progress over the period."
Australia and Pakistan will go head-to-head in a two-Test series in the United Arab Emirates in October.
Positive prognosis for Ryan Harris' dodgy knee
