Haber snapped his anterior cruciate ligament against Kilmarnock at McDiarmid Park on Saturday.
The 21-year-old Canadian came on as a late substitute in the 3-0 defeat but lasted only a few minutes before collapsing to the turf after turning awkwardly. Scans have revealed his season is over and manager Derek McInnes bemoaned the third such injury suffered by the club this season.
"Understandably, he is devastated by the news and our thoughts are with him," McInnes said. "But he's a young boy and at an early enough stage of his career where he can recover fully from this setback.
"From a St Johnstone point of view it is a huge blow, particularly as Marcus was invariably one of the three under-21 players we are required to have stripped and following on from Kevin Moon and Martin Hardie that is now three players who have suffered this injury.
"However, other players now need to show they can step up to the challenge of replacing Marcus."