Johnstone suffered the initial injury in the Valero Alamo Bowl last December and spent most of the spring season abstaining from contact in order to help his recovery.
Coaches were optimistic about his progress and an offensive line that returned five starters.
But with less than three weeks until Oregon's season opener against South Dakota, the Ducks will need to find a replacement for Johnstone, a 26-game starter who has protected Heisman candidate Marcus Mariota over the past two seasons.
Redshirt junior Andre Yruretagoyena, who took the first-team reps in the spring while Johnstone sat out, is the likely candidate.
"He's excited to get this opportunity," Mariota said of Yruretagoyena. "It is unfortunate the way it happened but sometimes guys are going to have to step up. Andre is going to do that for us and we're going to be prepared for that."
Yruretagoyena played in seven games last season for the Ducks, with his most snaps coming against Colorado (27) and in the opener against Nicholls State (26).
He spent most of the 2012 season on the scout team, but he did get into four games.
Mariota is confident that Johnstone will remain one of the team's leaders, especially with an offensive line that is now going through more transition than expected.
"Any time you have injuries, it's tough," Mariota said. "It is unfortunate. We're praying for him but he's going to work back to getting healthy and he's still going to make his contribution to our team."