It was the Ghanaian midfielder’s third Europa League goal this season.
He came on as a substitute in place of Nicolae Stanciu in the 64th minute and scored the goal less than a minute later after Lukasz Teodorczyk’s cross into the box found him in a position where all he needed was to dive in feet first ahead of his marker.
The hosts kept the score safe and qualified to the last eight 2-0 on aggregate.
Acheampong has scored five times in all competitions this season, with the Europa League yielding three goals and two in the Belgian Jupiler League.
He is the sole active Ghanaian remaining in the competition due to the injury that has kept Abdul Rahman Baba on the sidelines for Schalke since the Africa of Nations in January.
The draws for the next stage of the Europa League will be held on Friday, March 17.