Brazilian striker Malcom underwent a surgery to deal with his thigh muscle problem, an injury that has been treated with great discretion by the Russian club.
The operation was done in Finland. With two months of recovery expected, Malcolm will not return until 2020.
Malcom left Barcelona for Zenit in August but did not get off to a new start. After facing episodes of racism from a more radical faction of Zenit's own fans, the Brazilian suffered a thigh injury.
He has only played 64 minutes for Zenit.
In a statement previously, Malcom said, "I have a very delicate and sensitive injury. It seems that it hurts one day or two and then I don't feel pain, but when I shoot with a little more strength it hurts me again."