The Ghanaian registered his sixth goal of the campaign as the Eagles recorded their 13th win of the season.
The result temporarily leaves Niko Kovac's men fourth on the table ahead of Sunday's round of games.
It did not take long for Boateng to break the deadlock at Commerzbank-Arena.
Following a corner, the Ghanaian squeezed a shot over the line at the back post to put his side 1-0 up.
Luka Jovic then added a second in the 23rd minute, tapping home from close range when Ante Rebic, after a good work down the left, delivered a cross into the box.
From provider, Rebic turned finisher four minutes to half-time as he drilled a low shot from the edge of the box off the post and into the net, having been assisted by Marius Wolf.
For Boateng, it was his 26th league appearance and 22nd start for Frankfurt.
The 31-year-old joined the Eagles last summer on a three-year deal after terminating his contract with Spanish outfit Las Palmas.