The Ghanaian had two shots on target, one early in the game that goalkeeper Sergio Romero stopped and a header in extra time that was not strong enough to beat the goalkeeper.
Marcus Rashford scored the winner for the Red Devils in extra time after Sofiane Hanni had cancelled out Henrikh Mkhitaryan’s opener.
It was Acheampong’s 12th game of the Europa League where he scored three times this season. He scored a brace in Anderlecht’s 2-0 victory against Zenit St Petersburg as well as the lone goal in their victory against APOEL.
The European campaign ended for the Belgians who faced a tough task going into the game against United having never won in 18 previous attempts on English soil.
They will now turn their attention to the Belgian First Division playoffs where they lead the table six points ahead of Gent.
With Acheampong's exit from Uefa competition, Thomas Partey and Kwadwo Asamoah are the remaining Ghanaians playing in Europe.