The result ensured the 49ers (11-4) would have at least the equal best record outside the NFC's divisional winners by the end of the final round of matches next week.
That guaranteed them a post-season wildcard as they couldn't be overtaken by NFC West rivals Arizona (10-5) due to San Francisco's superiority in the divisional tiebreak.
The 49ers clinched the victory against the Falcons, in what was the final regular-season game at Candlestick Park, after NaVorro Bowman returned an interception 89 yards for a touchdown with 1:10 remaining in the contest.
The match-winning play occurred after Tramaine Brock broke up a pass intended for Harry Douglas.
Bowman then pounced on the ball, took off and extended the 49ers' league-best active winning streak to five matches.
The contest was full of fluctuations as the hosts led 3-0 at the first change, before the Falcons turned the table in the second quarter to lead 10-3 at half-time.
The pendulum then swung back in San Francisco's favour as they enjoyed a 13-10 buffer at three-quarter time and they ended an action-packed final period with their noses in front.
Atlanta (4-12) finish their disappointing campaign against Carolina next week.