Johnstone, a three-year starter, suffered the injury during practice last week and will have surgery Friday, he told CSNNW.com.
He had injured the same ACL during the Ducks' Alamo Bowl victory against Texas and had hoped to play in the season opener against South Dakota on Aug. 30.
Oregon has been picked to win not only the Pac-12 North but also the league championship by the media who cover the conference. The Ducks rank consistently in the top five in most preseason polls.
The Associated Press contributed to this report.