The Manchester United youngster opened the scoring against the run of play against Faroe Islands, finishing beautifully when Louie Annesley laid the ball into his path.
The hosts hit back, equalising with 19 minutes left, through Arni Frederiksberg, and then grabbed the winner in the World Cup qualifying Group L clash with Patrik Johannesen's late effort.
Scanlon's previous goal for his country was a header, against Liechtenstein, last September.
Meanwhile, Sekou Kone's Mali Under-20s side were knocked out of the Maurice Revello Tournament in Toulon.
The midfielder claimed an assist in a 2-2 draw with Saudi Arabia and, although Kone's side won the penalty shootout and earned a bonus point, they still exit the competition on goal difference.