Scans have shown Steven Smith has suffered an injury to the cervical facet joint in his neck after first reporting pain on the fourth day in Gqeberha, Cricket Australia (CA) has said, but he is expected to be fit to face New Zealand in early December after being ruled out of the decider against South Africa at Newlands.

Smith was hampered during his first innings at St George's Park and was pushed down to No. 7 in the second. It's understood Smith underwent scans on Friday when the team arrived in Cape Town. Cervical facet joints are small joints located on the back of each vertebra in the neck and act to guide and stabilise movement.

While head coach Andrew McDonald and Pat Cummins both expressed confidence that Smith would be able to play at Newlands, he continued to struggle in training ahead of the final Test and on the morning of the game he decided he wouldn't be able to get through the game.

"Steve Smith developed neck pain on day four of the second Test in Gqeberha last week," a CA statement said late on the second day's play. "Subsequent MRI imaging confirmed a cervical facet joint injury. Due to this and his limited range of motion he was unfit to participate in the current Test.

"Steve will continue to receive treatment and rehabilitation, with a full return to availability anticipated for the upcoming home Test series against New Zealand."

Smith has six weeks to recover for the New Zealand series, which begins on December 9 in Perth. Depending on his progress, there would be a window for him to play a Sheffield Shield match with New South Wales having their games starting on November 11 (against South Australia) and November 22 (against Queensland), with both being held in Sydney.

Smith's absence for the deciding Test saw Josh Inglis hastily brought into the side to bat at No. 5 with Cameron Green taking the No. 4 spot. Inglis finished the second day unbeaten on 85 off 111 balls while Green made 65, adding 126 with Matt Renshaw for the third wicket.

"I think to come in today, we were under a little bit of pressure having lost two quick wickets. The way that he [Inglis] played was really positive," Renshaw said. "It was a very Josh innings and I think it was really what we needed at that time."