On his return to Berlin, where he was born and made his breakthrough as a professional, the 30-year-old scored in the 80th minute to hand Niko Kovac's men a 2-1 away triumph.
Davie Selke and Marius Wolf cancelled out each other in the first half.
"We're really happy to have won a tough game on the road," Boateng said, as reported by his club's official website.
"It was an important win, particularly considering that we welcome Bayern next week.
"Because I'd picked up a booking early on, we had to consider whether it was worth me coming off at half-time, but the coach said that with my experience, I'd know which challenges to avoid.
"That worked out well."
Three points take the Eagles to eighth on the table, four positions above Sunday's opponents.
Boateng has now taken his season goal tally to three in 14 league games involving 12 starts.
The Ghana international, who joined Frankfurt in August, made his professional debut for Hertha in August 2005, coming on as a substitute - against none other than the same side he represented and scored for on Sunday.