As the tourists moved to 222-4 - 12 behind - on day two, 24-year-old Stokes had a scan on his right shoulder.
The results are not expected until Tuesday, when a decision will be made on if he can bat in the remainder of the match.
England need to win the third Test to avoid a series defeat.
Durham's Stokes was injured in the evening session of the first day, landing awkwardly after diving in an attempt to take a catch.
He left the field with his arm in a sling and has played no part since. Stokes was due to bat at number six, with wicketkeeper Jonny Bairstow promoted one spot in his place.
"Ben Stokes is alright but absolutely gutted," said England batsman Ian Bell. "He's going around with a smile on his face. Hopefully it's not as bad as people think."
Stokes is not part of the England squad for the four one-day internationals and three Twenty20 internationals that follow the Test series against Pakistan.
If the injury is serious, it may prevent him from being part of the squad for the four Tests in South Africa, the first of which begins on 26 December.
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England all-rounder Ben Stokes will not bowl again in the third and final Test against Pakistan after suffering a shoulder injury on day one in Sharjah.