In a cruel blow for Kruse, who missed most of last season including the World Cup after tearing the anterior cruciate ligament in his left knee, he faces about four months on the sidelines with ankle ligament damage.
It was feared the 26-year-old had injured his Achilles tendon in the second half of Australia's 2-1 victory over South Korea on Saturday, which saw it crowned the king of Asian football.
Typically, Achilles tendon injuries take 12 months of recovery.
But in a press conference on Tuesday, Leverkusen coach Roger Schmidt said the lay-off was likely to be about four months.
"This is really bitter for him, especially as he showed good form again," Schmidt said.