Playing against his younger brother Jerome, Boateng lasted for the entire duration as the Bavarians claimed a 1-0 away triumph at the Commerzbank-Arena.
Chile international Arturo Vidal scored the only goal on 20 minutes.
"I'm very proud and very satisfied," Boateng said, as reported by his club's official website.
"We played almost perfectly for 90 minutes. The team deserves huge credit for that.
"We ran, we fought, we played football and got the crowd behind us – you can't do any more than that.
"It's sad to lose a game like that but we've got to look forward. We played exactly the way we planned to. The coach prepared us perfectly.
"The only thing missing was a good result, the final pass or the last centimetre. It was nice to watch.
"We dozed off a bit at the back post for their goal, but these things happen."
Eyes set on playing in the Europa League next season, Frankfurt still linger around the qualification spot as they currently sit ninth on the table - only two places below the all-important line.
The Eagles now aim to promptly return to winning ways when they play away to Hamburg on Tuesday.