The Major League Soccer team made the announcement a day after the Portland midfielder and Canadian international was stretchered off in the first minute of a game against Toronto FC.
Johnson is expected to miss approximately six months.
The injury occurred just moments after kickoff as Johnson and Toronto FC defender Mark Bloom collided legs while going to the ground for a loose ball near midfield.
Johnson was taken off the field after a lengthy delay. Toronto midfielder Michael Bradley, a close friend of Johnson's, stood by as the Portland player was treated before leaving on a stretcher and taken to hospital.
There was no call on the play.
Johnson has made 29 appearances for the Timbers this season, recording six goals and two assists while earning MLS all-star honors for a second consecutive year.