Coach Dav Whatmore said the tourists were weighing up a replacement for the 24-year-old, who has failed to recover from a thigh injury sustained before Pakistan's practice match against the Emerging Cape Cobras.
"Junaid is definitely out of the second test but we hope to have him fit again for Centurion," Whatmore told a news conference.
The third Test at Centurion starts on February 22.
Seamer Mohammad Irfan or left-arm spinner Abdur Rehman are the front-runners to replace Khan in the line-up, with Whatmore saying the decision would be made once they had assessed the wicket on Thursday.
The coach also hinted that both might get to play, with the place of first-test debutant Rahat Ali under threat after he proved ineffective against the South African batsmen in the first test at the Wanderers, which the home team won.
If Irfan does feature, he would be making his test debut at the age of 30. Whatmore said his 7-40 in the practice match had suggested he was in the right form.
"Irfan had a good practice match, he did as much as he can to push for a game. If he does play in the second test he would have earned it."
Pakistan may opt to add a third spinner in Rehman, especially after the success that Mohammed Hafeez had at the Wanderers in picking up 4-16 in the first innings. He bowled well in tandem with front-line spinner Saeed Ajmal.
Whatmore confirmed that the batting line-up would remain the same from the first test, with Nasir Jamshed able to train on Tuesday after he missed the practice match with an ankle injury.
- Sports & Recreation
- Dav Whatmore
- Mohammad Irfan