The Bayer Leverkusen forward was injured at training on Friday and scans on Saturday confirmed he had torn his anterior cruciate ligament in his left knee and would miss the rest of the season, his Bundesliga club said.
Similar injuries have required up to a year of rehabilitation for other athletes, though local media have reported the 25-year-old was considering a different procedure that could see him playing again in three months.
The ligament augmentation and reconstruction system (LARS) uses synthetic components to repair the damage, though its long term success and effects are still unclear.
Kruse was seen as the linchpin of Ange Postecoglou's attack for the World Cup, where they open their Group B campaign against Chile in Cuiaba on June 13. The Netherlands and world champions Spain are also in the group.