Bowman put in a seven-tackle, one-sack performance to continue his recent trend of saving some of his best performances for matches against the 49ers NFC South rivals.
He admitted that he eagerly anticipates every clash with the Falcons, and revealed his relief at the progression of his recovery from a knee injury.
"It was fun," he told the 49ers official website. "I always look forward to playing them.
"My knee is getting there. That is what I want to keep hearing, that I am starting to look like the normal me. I told you guys that it was going to be a process, it was not going to happen overnight. I am pleased with the progress that I have made so far, but there is still more out there for me to do.
"I wanted to go into this bye week feeling like I left it all on the field, understanding that we have a week off. We showed that we can be a good team and can play great."
Sunday's victory improved San Francisco's record to start the season to 3-6, although they remain bottom of NFC West.