Running back Jordan James was fined $6,194 for unnecessary roughness involving the use of his helmet, while linebacker Dre Greenlaw received a $12,537 fine for unnecessary roughness involving striking an opponent.
The two fines total $18,731.
James, a fifth-round pick in the 2025 NFL Draft, saw limited offensive opportunities against Atlanta, recording a six-yard carry and an 11-yard reception.
Greenlaw, meanwhile, finished with 12 tackles, including four solo stops, in the 29-20 defeat. It tied his season-high tackle total.
Greenlaw's penalty reportedly stemmed from an attempt to deliver a "Peanut punch" to force a fumble by Falcons wide receiver Drake London. However, his punch struck London's helmet instead.
No flag was thrown on the play.
The fines come after a frustrating afternoon for San Francisco, which committed four turnovers and allowed Atlanta to score 23 unanswered points after building an 11-point lead. The loss ended the 49ers' unbeaten start to the season, dropping them to 6-1.
San Francisco is off this weekend for its Week 8 bye but will return to action in Week 9. The 49ers host the Las Vegas Raiders at Levi's Stadium on Sunday, November 8.
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