SANTA CLARA, Calif. -- The San Francisco 49ers' playoff drought is over. But it didn't happen how they wanted.

For the first time since 2013, the 49ers are headed to the postseason, but they needed some help to get there after a 29-22 loss to the Atlanta Falcons on Sunday at Levi's Stadium.

Atlanta quarterback Matt Ryan drove the Falcons 70 yards in the closing moments to throw a 5-yard touchdown pass to Julio Jones with two seconds left. Jones caught the ball at the goal line and was initially ruled short, but a review overturned it for a touchdown. The score put the Falcons ahead 23-22, and Atlanta scored again as time expired when Olamide Zaccheaus returned a failed lateral attempt by the 49ers for a touchdown.

Sunday's loss made the Niners the first team to win 10 games in a season and also lose at least three games in the final 10 seconds of regulation and overtime since the 2000 Philadelphia Eagles, according to ESPN Stats & Information.

Despite the loss, the 49ers clinched a playoff spot by virtue of the Los Angeles Rams' 44-21 loss to the Dallas Cowboys. The Seattle Seahawks (11-3) and Green Bay Packers (11-3) also clinched playoff spots with their victories Sunday combined with the Rams' loss.

Although the 49ers acknowledged that breaking their playoff drought was a step in the right direction, the overwhelming feeling in the locker room was one of disappointment that it came with some help rather than their own victory.

"I'm glad we're in," coach Kyle Shanahan said. "It starts with that. That's cool but doesn't make me feel better right now."

The defeat dropped the 11-3 Niners into a tie with the Seahawks atop the NFC West division, with Seattle holding the tiebreaker because of its win against the Niners earlier this season. The Niners currently sit in the fifth spot in the NFC playoff picture and would have to go on the road to open the postseason if the season ended Sunday.

Fortunately for the Niners, who are 3-3 in their past six games, the season didn't end Sunday.

Coming off a 48-46 win against New Orleans after which five key players were ruled out this week or longer because of injuries, the Niners were noticeably sluggish on Sunday.

In addition to the attrition, the Niners were coming off a three-game gantlet against Green Bay, Baltimore and New Orleans, with the latter two on the road in a 10-day trip that included a stop in Bradenton, Florida, for the week of practice between the Ravens and Saints game.

While Shanahan didn't see signs of a letdown, multiple players believed there was a drop off in intensity from last week in New Orleans to this week against the Falcons, who entered at 4-9.

"We for sure could have came out with a little more juice as a team in general," linebacker Fred Warner said. "I was trying to get us going a little bit but even myself, I felt like I still could have brought even more early on in the game and as the game went on. I always look at myself when it comes to that kind of stuff on defense me bringing that juice and the energy."

Tight end George Kittle was one of the few bright spots, doing most of the heavy lifting for the offense. Kittle set a career high for catches in a game with 13, coming on 17 targets, to go with 134 yards. In the process, Kittle moved into first place for most receiving yards by a tight end in his first three seasons, passing Jimmy Graham, Rob Gronkowski and Mike Ditka. Kittle now has 2,780 receiving yards for his career.

But it was the one play Kittle made that left him upset after the game. On third-and-4 at Atlanta's 28 with 1:59 to go, Kittle caught a quick pass in the right flat from quarterback Jimmy Garoppolo and turned upfield.

With the first down marker in his sights, Kittle attempted to switch the ball to his opposite hand so he could extend a stiff arm. He lost the ball and recovered it at Atlanta's 25, a yard short of the first down. Instead of a first down and the chance to essentially run the clock out, the Niners settled for a field goal that left time for Atlanta to drive for Jones' winning touchdown.

"Just dropped it," Kittle said. "Tried to switch hands so I could stiff arm him. It didn't work out well for me.

"I wish I could play right now. It's a sour taste, I'd love to get it out of my mouth right now. We've got 24 hours to flush it and get back to work."

When Kittle wasn't providing the offense, the Niners struggled to get much of anything else going. Fullback Kyle Juszczyk's 2-yard touchdown catch gave the Niners a 19-10 lead in the fourth quarter, but they coughed it up with the Falcons scoring three touchdowns in the final 5:15.

After finishing 2018 at 4-12 and picking second in last year's NFL draft, San Francisco still remains in control of its playoff positioning. The 49ers close out the season at home against the Rams on Saturday followed by a potential clash for the NFC West and the NFC's No. 1 seed against the Seahawks in Seattle on Dec. 29.

Despite the loss, if the 49ers win those final two games, they would not only win the division, but also wrap up the NFC's top seed and home-field advantage through the NFC portion of the playoffs. San Francisco holds head-to-head tiebreakers against the Saints and Packers, the other two top contenders in the NFC aside from the Seahawks.

"That (playoff berth) is something to be proud of, but no it does not (feel good)," tackle Mike McGlinchey said. "We would have liked to have been in on a victory and have done that. Unfortunately, we didn't, but we're in the dance now and we got to close out these next two weeks and hopefully put ourselves in position for a nice road to the Super Bowl."