The Falcons took advantage of the 49ers' plethora of absentees, quarterback Marcus Mariota completing 13 of his 14 pass attempts and accounting for three touchdowns.
Kyle Shanahan felt the San Francisco 49ers had opportunities to overcome their swathe of defensive injuries and avoid defeat to the Atlanta Falcons.
The 49ers were favoured to move 4-2 with victory in Atlanta, but instead fell to a 28-14 defeat at Mercedes-Benz Stadium.
Starting cornerback Charvarius Ward suffered a groin injury in the loss, a week on from fellow starter Emmanuel Moseley sustaining a torn anterior cruciate ligament in the blowout win over the Carolina Panthers.
On defense, the Niners entered the game without star pass rusher Nick Bosa (groin), Javon Kinlaw (knee), and Arik Armstead (foot), as well as linebacker Azeez Al-Shaair (knee) and safety Jimmie Ward (hand). Edge rusher Samson Ebukam battled injury throughout the game.
The Falcons took advantage of the 49ers' plethora of absentees, quarterback Marcus Mariota completing 13 of his 14 pass attempts and accounting for three touchdowns.
Mariota is the third player in NFL history to record at least two touchdown passes, one rushing touchdown and a completion percentage of 90-or-higher (minimum 10 attempts) in a single game, joining Ryan Fitzpatrick (September 24, 2020) and Frank Ryan (December 12, 1964).
The 49ers entered the game allowing just three yards a carry but gave up 168 yards rushing against the Falcons.
San Francisco fell 14-0 behind but recovered to tie things up at 14-14 through a pair of Brandon Aiyuk touchdowns.
"I think we had our chances to overcome," Shanahan said. "We made it harder on ourselves. I'm not taking anything away from them.
"Yeah, that's a big deal missing those people, but we had every chance to still pull that off."
Tight end George Kittle echoed his coach's sentiments, adding: "You could use [injuries] as an excuse but we're the San Francisco 49ers."We have a standard that we play at. We play at a very high level, a lot of energy, 100 percent effort on every single play. I haven't watched the tape yet, but I don't know that we gave that at every single position.
"We had a lot of young guys play. We're missing a lot of guys. We've just got to make sure we're playing at that level every single snap or that's going to happen, especially when you are down guys."
Linebacker Fred Warner said of the Falcons' approach: "We knew exactly what they were going to do. That was the challenge for us on defense was to stop the run and to dictate that.
"But I've got to give them props for dictating the entire game in the run game. We were getting knocked back, me included, and we've just got to be better up front in the front seven.
"It [the injuries] does suck. You wish you have your guys out there, but at the same time, I feel like for me, I put a lot of pressure on myself in the fact that I command the defense.
"I'm the one who should get all 11 lined up at all times regardless of who's out there, and everybody else who's coming into the game, they've got to be ready to go no matter what. It's all about being prepared. Regardless of the circumstance, whoever's out there we've got to make sure we're playing to our standard."
The 49ers have consistently battled injuries during Shahanan's tenure, overcoming them to reach the Super Bowl in the 2019 season and the NFC Championship Game last term. In 2020, the Niners finished 6-10 after a year in which they were decimated by injuries and COVID issues.
"The five years I've been here, this isn't anything new. I've seen it," said Warner. "At some point you've got to adjust and guys have got to be ready to go no matter the situation. We've got to find ways to win regardless of the circumstance."