Schalke said in a statement that Farfan, who has scored 22 goals in 102 Bundesliga appearances, had torn an anterior ligament in his knee and would have to rest for four weeks before starting two weeks of strengthening work.
In another blow for Huub Stevens's team, captain Benedikt Hoewedes sustained a similar injury in Germany's 3-0 win over Netherlands.
He limped off injured during the second half of Peru's 2-0 defeat in Quito on Tuesday, although returned to the pitch to join in a melee following the final whistle.
Schalke, fifth in the Bundesliga, said the length of Hoewedes's absence would be known after tests on Thursday.
In another blow for Huub Stevens's team, captain Benedikt Hoewedes sustained a similar injury in Germany's 3-0 win over Netherlands.
He limped off injured during the second half of Peru's 2-0 defeat in Quito on Tuesday, although returned to the pitch to join in a melee following the final whistle.
Schalke, fifth in the Bundesliga, said the length of Hoewedes's absence would be known after tests on Thursday.
