SAN FRANCISCO -- San Francisco 49ers quarterback Blaine Gabbert waited over two years to start another game in the NFL after losing his starting job with the Jacksonville Jaguars in 2013.

He made the most of his opportunity Sunday.

Gabbert threw for 185 yards and two touchdowns, leading the 49ers to a 17-16 victory against the Atlanta Falcons at Levi's Stadium.

Gabbert replaced Colin Kaepernick in the starting lineup and made his first start since Oct. 6, 2013, with Jacksonville. He completed 15 of 25 passes with two interceptions.

"It was wonderful," Gabbert said. "I'm so appreciative of this opportunity. I just wanted to go out there and compete, lead these guys. I just wanted to go out there today and have fun. You play well when you're having fun. That was the biggest thing."

Tight end Garrett Celek caught two touchdown passes for the 49ers (3-6), and running back Shaun Draughn, who signed with the team as a free agent earlier in the week, carried 16 times for 58 yards.

Quarterback Matt Ryan completed 30 of 45 passes for 303 yards and one touchdown for the Falcons (6-3), who lost their second straight game and fell for the third time in their past four games. Wide receiver Julio Jones caught 10 passes for 137 yards.

"I think you always expect something better after you play poorly," Ryan said. "We didn't do it today, though. We didn't play up to the way that we're capable, and I think San Francisco did a nice job. They played well defensively."

The question for the 49ers is whether Gabbert played well enough to keep the starting job and face Seattle on Nov. 22 after a bye week.

San Francisco coach Jim Tomsula said he's not ready to make that decision.

"Gabbert was our starter today, and I don't have a comment past that," Tomsula said.

Falcons rookie defensive end Vic Beasley Jr. intercepted a Gabbert pass intended for tight end Vance McDonald at the Atlanta 33 with 7:14 left to play and San Francisco leading 17-13.

Ryan completed six of his next seven passes, marching the Falcons to San Francisco's 8, where they had first-and-goal. On third-and-goal from the 4, Ryan hit wide receiver Justin Hardy over the middle, but safety Jimmie Ward cut him down at the 1.

Instead of going for it fourth down, Atlanta settled for Matt Bryant's 19-yard field goal with 2:56 left to play, cutting San Francisco's lead to 17-16. The Falcons never got the ball back.

"The sequencing at the end of the game, the fourth-down play I chose to kick it there," Falcons coach Dan Quinn said. "I thought we would get the kick, get the stop defensively, then use our time outs and then go attack on offense. We're a really good two-minute offense. So that was the reasoning behind it. I felt like we were stopping them defensively and could do it again and go win that way."

The 49ers took over at their 20 with 2:51 to play. On third-and-4 from the 26, Gabbert ran a bootleg around right end for 5 yards, giving the 49ers a first down with 2:00 left to play. The 49ers got one more first down and ran out the clock.

"It was a play that we'd been working on all week, kind of that we were going to go to at crunch time," Gabbert said. "Our offensive line did a tremendous job selling the power to the left. It was a run-pass option, but once I knew we had the defensive end sealed and it was me on the (defensive back), I was just going to go for the first down regardless."

San Francisco linebacker NaVorro Bowman said that Gabbert gave the entire team a boost of energy.

"Blaine had to approach it free-minded, go out there and give it his best shot," Bowman said. "We wanted to rally around him and not think, 'OK, the backup quarterback's our quarterback, we're not going to win.' We still approached the game the same way as if (Kaepernick) was in there and rallied around Blaine. He did a great job today.

"He definitely led us and played for us today. Our hats go off to him and I'm looking forward to what's coming down the road next."

San Francisco's defense held Falcons running back Devonta Freeman to 12 yards on 12 carries.

Gabbert completed 10 of 16 passes for 115 yards and two touchdowns in the first half, leading the 49ers to a 17-13 advantage.

The Falcons, however, had struck first, taking a 3-0 lead with 9:25 left in the opening quarter on Bryant's 44-yard field goal, capping a 46-yard drive.

The 49ers moved ahead 7-3 on Gabbert's 1-yard touchdown pass to Celek with 13:41 remaining in the half. San Francisco marched 84 yards on six plays for the score. Gabbert's 41-yard pass to wide receiver Quinton Patton was the biggest play on the drive.

"With him not playing the whole year and then to step in like this and do what he did, I think he's a really good player and he's a tough guy," Celek said of Gabbert.

San Francisco extended its lead to 10-6 on Phil Dawson's 44-yard field goal with 3:20 left in the half, and the 49ers made it 17-6 when Gabbert fired an 11-yard touchdown pass to Celek with 1:11 showing.

Atlanta answered with a 78-yard, three-play touchdown drive capped by Ryan's 17-yard scoring pass to Freeman with 13 seconds left in the half. Ryan opened the drive with a 54-yard deep strike to Jones, giving Atlanta a first down at the 49ers' 24.

NOTES: Starting 49ers CBs Tramaine Brock (shin) and Kenneth Acker (chest/concussion) were inactive. Dontae Johnson and Marcus Cromartie started in their place. ... 49ers backup CB Keith Reaser (ankle) was also inactive. ... Falcons starting CB Robert Alford (groin) and S William Moore (groin) were inactive. CB Jalen Collins and S Kemal Ishmael started. ... OLB Philip Wheeler started for Atlanta in place of Justin Durant (calf), who was inactive. ... Falcons backup S Robenson Therezie sustained a hamstring injury in the first quarter and did not return.