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The five-time Ballon d'Or winner netted his 800th and 801st career goals against the Gunners as United ran out 3-2 winners under caretaker boss Michael Carrick.
TV personality Morgan, who is a Gunners fan, has interviewed Ronaldo in the past and sent him a message prior to the game.
He said in his Daily Mail column: “Arsenal played Manchester United and I sent Cristiano Ronaldo a desperate plea before kick-off, ‘Please don’t score against us…'
“Of course, he scored twice, and United won 3-2. ‘Sorry,’ Cristiano texted back after the final whistle.
“I would have accepted the apology if it hadn’t also contained a laughing emoji.”
Since returning to Old Trafford in the summer, Ronaldo has been a focal point in attack with 13 goals in 18 games.
Many wondered if he'd fit in under interim manager Ralf Rangnick, but it's proven to be no problem.
The 36-year-old scored on Saturday evening as United ran out 1-0 winners against Norwich City.
Max Aarons dragged Ronaldo down in the box and he smashed past Tim Krul with no issue.
United have moved up to fifth in the Premier League and are now one point behind West Ham in the top four.
A scary moment in the second half saw Victor Lindelof substituted after holding his chest and appearing to have chest problems.
Lindelof received medical attention from the Carrow Road medical staff and was substituted for Eric Bailly with 16 minutes to go.
David de Gea had a clear view of the situation and spoke to Sky Sports about it post-match.
The goalkeeper said: "Yeah [being concerned], especially when we've seen some players feeling a bit with their breathing," De Gea told Sky Sports after the full-time whistle.
"We saw already [Christian] Eriksen, [Sergio] Aguero ... so it is sometimes a bit difficult to see your player acting like this so it was better to change. I hope he is completely fine.
"As soon as it was like, difficult breathing and feeling strange, the game doesn't matter.
"First of all is life. Football doesn't matter. We saw some players who are feeling a bit, I don't know what was going on, but Victor was feeling his breathing."