The Armenian appeared to be clutching his hamstring as he went off to be replaced by Marcus Rashford and could be a doubt for the EFL Cup final against Southampton on Sunday.
In the end it was comfortable for United but they will be without Eric Bailly in the first leg of the next round after he was sent off for two bookable offences.
The Ivorian, who was already one yellow away from suspension, will be available for the second leg but will still be one caution away from missing another game.
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Direct link to this article: https://www.armenianclub.com/2017/02/22/st-etienne-0-1-man-united-mkhitaryan-scores-but-limps-off-injured/