Opening batsman Anwar has been ruled out of both the team's warm-up matches after ending up in hospital following a blow on the left elbow.
Team manager Shahryar Khan said: "He was hit while batting in the nets and had two scans. There's no fracture, it's just bruising. He's out for three or four days.
"Anything from Shoaib hitting the body is pretty lethal."
Pakistan are playing Gauteng in Lenasia, just outside Johannesburg, in their first warm-up
Shoaib, challenging Australia's Brett Lee as the fastest bowler in the world and dubbed the 'Rawalpindi Express', was unofficially timed bowling at 100.04mph (161kph) last year.
The 34-year-old Anwar, the holder of the world record one-day score of 194, has just been recalled to the team after a long spell in the wilderness in an attempt to bolster Pakistan's batting.
Pakistan play their opening match against Australia, a repeat of the 1999 World Cup final, on February 11 at the Wanderers ground in Johannesburg.