Midfielder Hughes finished off a counter-attacking move from a corner in the first-half.
He was one of four trialists to represent the Iron in the match, along with Tom Newey, Matty Mainwaring and Yani.
It completed the tour of the Republic of Ireland for Alan Knill's side, who also defeated Bray Wanderers by a single goal on Tuesday night.
The Iron will fly back to the United Kingdom on Friday, with the next pre-season game against Grimsby Town on Tuesday evening.