Khawaja, who is under pressure to keep his place, got his knee caught in the outfield while fielding during the final session on Thursday.
The left-handed batsman tried to slide to field a Dawid Malan drive but instead saw his knee jar before he limped off.
England were 160-3 at the time with Malan (28) and captain Joe Root (42) at the crease.
Khawaja returned to the field four overs later.
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