John York refutes report; Kelly explains Christian Ponder’s promotion

San Francisco 49ers Chief Executive Officer Jed York in a file photo, Jan. 4, 2016. (AP Photo/Ben Margot) San Francisco 49ers Chief Executive Officer Jed York in a file photo, Jan. 4, 2016. (AP Photo/Ben Margot) Photo: Ben Margot, Associated Press Photo: Ben Margot, Associated Press Image 1 of / 8 Caption Close John York refutes report; Kelly explains Christian Ponder’s promotion 1 / 8 Back to Gallery

ATLANTA — After the 49ers’ 41-13 loss to the Falcons on Sunday, 49ers owner Dr. John York said a report that his son, CEO Jed York, could be stripped of some of his power is “completely” false.

York made the assertion to the San Jose Mercury News and Sacramento Bee outside the 49ers’ locker room after the team’s 13th straight loss. Last week, CBS Sports reported John York and his wife, Denise DeBartolo York, might take a more “hands-on approach,” with their son possibly being moved out of football operations. The CBS report subsequently was disputed by ProFootballTalk.com.

Jed York is under fire after parting ways with Jim Harbaugh after the 2014 season and hiring Jim Tomsula and Chip Kelly, who have combined for a 6-24 record the past two seasons.

Ponder promoted: After he was inactive for the first 13 games, Christian Ponder replaced Blaine Gabbert as the 49ers’ No. 2 quarterback. Gabbert was inactive for the first time in his three-year tenure with the 49ers.

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Kelly said Ponder earned his promotion by his performance with the scout-team offense.

“We’ve seen him in practice do some really good things,” Kelly said. “… I think he and Blaine are battling.”

Despite the lopsided score Sunday, Ponder didn’t play against the Falcons. Kelly said Ponder wasn’t promoted with an eye toward playing him before the end of the season.

“We’re trying to win football games,” Kelly said. “This isn’t open tryouts right now.”

Ponder and Gabbert are in the final year of their contracts, and Colin Kaepernick has an option to become a free agent.

Ponder won a roster spot this summer by leading two comeback victories in three preseason games. He completed 16 of 25 passes for 198 yards with a touchdown and interception, and added three rushing scores.

Hodges inactive: A team spokesman said starting inside linebacker Gerald Hodges was inactive because of an unspecified violation of team rules, but Kelly offered only that it was a “coach’s decision.”

Hodges declined to speak with reporters after he left the locker room following the game. Kelly declined to say if Hodges would play Saturday in Los Angeles.

“It was a coach’s decision,” Kelly said. “I can’t expand on that any more.”

Hodges entered Sunday ranked third on the team in tackles (66) and sacks (three). He also has a team-high two interceptions.

Injury report: Wide receiver Quinton Patton had an orthopedic boot on his left foot, and tight end Blake Bell (shoulder) and inside linebacker Nick Bellore (elbow) each had an arm in a sling after the game.

Center Marcus Martin (ankle) and cornerback Jimmie Ward (shoulder) also didn’t finish the game. Martin’s left ankle was heavily taped in the locker room.

Wrong records: The 49ers allowed 248 rushing yards and in doing so, broke the franchise record for most rushing yards allowed in a season.

They have allowed 2,468 rushing yards, 105 more than in 1978, when they finished 2-14. If they surrender 20 points and 311 yards in their final two games, they also set will franchise record for points and total yards allowed.

Eric Branch is a San Francisco Chronicle staff writer.