England's 64-run defeat by world champions Australia was overshadowed by the controversy that ensued early in the 26th over of their run chase.
Stokes, went down the pitch and played a Mitchell Starc delivery back to the left-arm fast bowler, who then aimed a powerful throw back in his direction as he tried for a run-out.
As Stokes leaned back and turned to make his ground, the ball hit the Durham all-rounder's arm.
Batsmen are allowed to protect themselves but they must not, under the Laws of Cricket, "wilfully" obstruct the field.
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Stokes told ESPN Cricinfo on Monday: "A guy was standing there five feet away from me and it was just a complete reaction.
"I didn't put my hand there wilfully, it was purely out of human reaction to protect myself. But the decision was made, there's nothing I can do but it wasn't wilful whatsoever.
The series continues at Old Trafford on Tuesday, with Australia 2-0 up with three to play.