The attacker was on the score sheet as The Eagles registered a 2-0 home win at Commerzbank-Arena.
The 30-year-old has now taken his season goal tally to four in the topflight.
On his 20th league appearance for Niko Kovac's outfit, Boateng broke the deadlock two minutes to half-time.
The attacker scored from close range on the assist of Timothy Chandler, who delivered a cross from the right.
The Ghanaian almost turned villain after recess when he fouled Lars Stindl inside the box for a penalty.
But Thorgan Hazard's spot-kick only came against the crossbar, leaving the home side off the hook.
The game looked headed for a 1-0 win for Kovac's charges until the second minute of injury time when Luka Jovic struck to make it 2-0.
The victory temporarily takes Frankfurt to second on the league table ahead of Saturday's round of matchday 20 games.
The Eagles play away to Augsburg in their next fixture.
Boateng joined Frankfurt in the summer on a three-year deal.