Schalke's second straight win was sealed by the Ghana international's strike in only his second game since joining from AC Milan in the summer.
It was the highlight of an otherwise flat, tactical affair at the Coface Arena with Schalke defending their lead resolutely to inflict a second straight defeat on Mainz.
The hosts began brightly with Eric-Maxim Choupo-Moting inspiring in their attacking play.
Schalke, who were without the rested Jermaine Jones, who was tired after returning from international duty with the United States, lacked somebody to take the initiative in the middle of the field.
When they did attack, Jefferson Farfan and Julian Draxler both wasted chances while Choupo-Moting could have had a hat-trick at the other end.
Boateng then decided to take matters into his own hands with a shot out of nothing which left Heinz Muller no chance, and proved to be decisive.
Dennis Aogo went close to making it two with Schalke's best chance of the second half, but Jens Keller's men spent much of the second 45 minutes desperately defending their lead.
Mainz could not find a way through, though, and when goalkeeper Heinz Muller raced up for a late corner, Draxler wasted the chance to make it two on the break with the goal gaping.
However, a second goal was not necessary as Boateng's strike was enough to lift Schalke into the top half of the table.