The left-hander was hit by a short ball from Australia left-arm fast bowler Mitchell Starc in the seventh over of the match having scored one run and faced seven deliveries.
The England and Wales Cricket Board confirmed that Morgan, 29, is "being treated for concussion and will take no further part in the game".
Australia's players immediately surrounded Dublin-born Morgan after he received the blow and following treatment by the England medical staff on the pitch the 29-year-old climbed to his feet and made his way back to the dressing room.
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