The former Chelsea striker, who only recently returned to action following a stint on the sidelines, found the net in either half.
His first of the encounter was scored just one minute before the break when Theodor Gebre Selassie picked the Argentine out in the right side of the penalty area.
From there, Di Santo took one touch, before finding the top corner of Thomas Kraft's net.
He then made sure of the outcome 21 minutes from time, with Clemens Fritz the creator on this occasion.
It was his cross that found Di Santo, who sent an acrobatic effort bouncing into the far corner of the away side's goal.
The home side continued to dominate proceedings as the game drew to a close, but they were unable get the better of Kraft for a third time.