Ali, 30, suffered the infection during the Haj in Saudi Arabia last month. He played two of the three one-day internationals against Zimbabwe in discomfort before missing the final match.
Team manager Intikhab Alam said the management took the decision after seeing the extent of his infection before training on Sunday.
“Because of the injury Ali could not wear a shoe on his left foot so he couldn’t train as well,” Alam told AFP.
Since making his debut against Australia at Lord’s in Pakistan’s neutral-venue Test in 2010, Ali has featured in 44 Tests and scored 3,393 runs.
His absence could be an opportunity for former captain Shoaib Malik to play his first Test in five years.
Pakistan also have Fawad Alam in the squad but Malik’s ability to bowl off-spin will be an added advantage.
Malik was drafted into the Test squad as 16th member after showing good form with the bat in the 2-1 one-dayer series win over Zimbabwe last week.
The remaining two Tests in the series will be played in Dubai (October 22-26) and Sharjah (November 1-5). The teams will also play four one-dayers and two Twenty20 internationals.