The 28-year-old injured webbing on his bowling hand and a finger while catching a ball in training at the Sharjah stadium.
Team manager Intikhab Alam said Khan was taken to hospital for treatment.
“Imran Khan hurt his bowling hand and a finger so he was sent to hospital, where he got four stitches and he will take ten days to recover,” Alam told AFP.
The third Test starts in Sharjah from Sunday.
Khan, who made his debut against Australia last year, took six wickets in the two Test matches, four in Dubai where Pakistan won by 178 runs.
The first Test ended in a draw in Abu Dhabi.
Pakistan have the option of bringing in left-arm paceman Rahat Ali, who played in the first match.