In addition, Kelly made it clear that Colin Kaepernick will be No. 2 behind Gabbert and veteran Christian Ponder will be the team's third quarterback when the Niners open the season Sept. 12 against the Los Angeles Rams on Monday Night Football.
"Right now, I have met with our quarterbacks. Blaine is No. 1 and he'll start versus the Rams, and Kap is No. 2," Kelly said. "We'll only have two guys up [at quarterback] on game day."
It was always going to be an uphill climb for Kaepernick to win the job after he fell behind Gabbert in the spring because he was unable to practice as he recovered from thumb, knee and shoulder injuries. That allowed Gabbert to take the bulk of the snaps with the starters during organized team activities.
At the beginning of training camp, Kelly said there'd still be a competition between Gabbert and Kaepernick for the starting job. They split the first-team repetitions in the opening days of camp before right-shoulder tightness kept Kaepernick out of the first two preseason games and joint practices with the Denver Broncos and Houston Texans.
In preseason games, Gabbert led the 49ers to touchdowns on three of his eight possessions as he went 12-of-22 for 146 yards and a TD for a passer rating of 90.3. He also rushed for 33 yards on five carries. Kaepernick was 13-of-24 for 117 yards for a passer rating of 67.5 and led one touchdown drive. He rushed for 56 yards on eight carries.
Ultimately, Gabbert's ability to stay healthy and get valuable reps in Kelly's offense gave him the edge.
"I think his grasp and command of what we're doing, I think he's a good fit for what we want to get accomplished," Kelly said. "I have a lot of confidence in what he can do with us offensively.
"I think Kap is still coming off of getting himself healthy, 100 percent go. He has been cleared to play, but he still knows he's got some work to do. He's not up to his playing weight that he was when he was successful here, and he'll continue to work on that. He missed a couple weeks there with the arm [soreness] and that set him back a little bit in terms of his ability to compete for it, but the timetable was the timetable and right now we feel like Blaine is the starter."
Despite some outside discussion about whether Kaepernick would stick on the roster, Kelly said the plan all along was for the team to keep three quarterbacks. Last week, he said Kaepernick was one of the two best quarterbacks on the roster, and Kaepernick followed that up with a solid performance in the preseason finale.
Kaepernick's recent decision to sit or kneel during the national anthem in protest of racial oppression did not play a factor in the decision to keep him or make him No. 2 on the depth chart, Kelly said.
Kaepernick has said his protest is not meant to denigrate police, military or the country, but rather serves as his way of bringing attention to what he sees are failings in the United States.
Asked whether he had concerns about Kaepernick potentially dividing the team, Kelly stuck by the answer he's given the other times he's been asked similar questions.
"When he's here at 4900 (Marie P. DeBartolo Way), he's all about football and all about work, and that's what I've seen since he's been here," Kelly said. "He continues to display that every day he's in this building.
"How he's handled himself and how he's been with us, I have no issues with Kap at all."
In keeping Ponder, the 49ers have three quarterbacks taken in the first 36 picks of the 2011 NFL draft. Ponder signed with the 49ers after Thad Lewis suffered a season-ending knee injury in the preseason opener Aug. 14.
When the Niners called, Ponder said he had been painting his house, among other household chores. But Ponder acclimated quickly and won a spot.
"I think you need to have three [quarterbacks] in this league with the injury rate of quarterbacks," Kelly said. "I have never been comfortable with keeping two. I think you need to have three, and I think Christian's performance, coming in on a short week against Denver and how he played there and the performance of how he played last Thursday night against San Diego, gave him the opportunity to earn the No. 3 spot."