Here is a select list of online bookstores who sell a range of books. Note that I have not included the names of Pakistani publishers who only sell their own books through websites.
(online only; mainly used books)
(online + physical bookstores in Karachi and Lahore)
(online + physical bookstore in Lahore; both used and new books)
Saeed Book Bank
(online + physical bookstore in Islamabad)
(online + physical bookstores in Islamabad and Lahore)