All Blacks flanker Sam Cane's rugby season is over.

Cane suffered a small fracture in in his lower neck late in the first half of the All Blacks' 32-30 victory over South Africa.

The 26-year-old Cane underwent surgery overnight in Johannesburg to stabilise the injury which will allow the fracture to heal of its own accord.

The All Blacks tweeted last night that Cane will be out of action for several months but is expected to make a full recovery.

"All Blacks loose forward @SamCane7 is to have surgery in Johannesburg today after suffering a fracture in his neck in last night's Test against South Africa," the Tweet read. "[He's] expected to make a full recovery.

"All Blacks Doctor Tony Page said Cane had suffered a fracture in a vertebrae but thankfully had not suffered any nerve damage. Cane will stay in South Africa for the week before flying home. [He] will be out of rugby for several months."

Cane was one of the All Blacks' most influential players in the dramatic test in Pretoria before being forced to leave the game in the 35th minute after going down with a neck injury. He was able to walk off the field.

The injury means Cane will miss the All Blacks' Northern tour in November and it is unknown when he will be able to return next year.