The Ghanaian was sent off in stoppage time when he was shown a second yellow card.
He picked up his first booking on 70 minutes, six minutes after coming off the bench to replace Borja Mayoral.
Afena-Gyan was booked for a shoulder barge and then was sent off in the 94th minute, after having smashed the ball into the net.
He celebrated but the referee disallowed the goal for handball in the build-up and gave the striker his second yellow card.
Roma's goals were scored by Chris Smalling and Roger Ibanez - both headers as Mourinho's men returned to winning ways after two successive losses.
The 18-year-old was making a return to action having recovered from coronavirus that saw him miss Roma's last two games.
After a week in isolation, Afena-Gyan tested negative and was cleared to rejoin his teammates in training.
The red card although cruel is part of the learning curve for Afena-Gyan. He has eight goals this season - two for the senior team and six for U19 team. Read Full Story
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