The 36-year-old player was not punished by referee Eddie Ilderton during Saturday's match as he did not see it, but video evidence sent to the Football Association by the Iron resulted in the belated suspension.
It came after Scunthorpe were reduced to 10-men when captain Paul Reid was red carded for an alleged elbow, with an appeal failing to get the card overturned.
Notts County have said they will not appeal against Hughes' ban.