There is fear Broncos cornerback Chris Harris has suffered a serious knee injury.

One of Denver’s top defensive players, Harris left the game in the third quarter with ankle and knee injuries and did not return. Although X-rays were negative, Harris will undergo an MRI exam on his knee Monday morning. It’s almost certain Harris won’t play in the AFC championship game next week against Tom Brady and the New England Patriots.

Harris was replaced by veteran Quentin Jammer, and the former Charger was tested by former teammate Philip Rivers.

“I played like (crud),” Jammer said. “It wasn’t anything physical. It was mental. I was sitting on routes I shouldn’t have been sitting on.”

In Jammer’s defense, he hasn’t played much this year. The Broncos kept cornerback Champ Bailey in the slot and had Jammer play outside along with Dominique Rodgers-Cromartie.

The Broncos could also use Kayvon Webster and Tony Carter against New England.

Lesson learned. In trying to protect a seven-point lead late in the game, the Broncos did not run the ball on third-and-long. On third-and-17, deep in their own end, Peyton Manning passed … to a wide-open Julius Thomas near the Broncos’ sideline for a 21-yard gain.

“It was the perfect call,” Manning said, giving all the credit to offensive coordinator Adam Gase.

“It was a lack of communication on our part,” said San Diego coach and former Broncos offensive coordinator Mike McCoy.

Two plays later, it was third-and-6 with 2:12 left. Again, Manning hit Thomas for a first down.

“We didn’t want to punt the ball back to them and give them an opportunity,” Thomas said. “We knew that we needed to go out there and do what we needed to do so we could end the game in a victory formation. There’s no better feeling for an offense than to go out there and kneel to win the game.”

Manning said of his second-year tight end, the former Portland State basketball star: “Julius was huge all game. He’s been huge all season. … Julius and I have spent a lot of time working on those particular routes — after practice, in practice.”

Decker punt returns. The Broncos took punt return duty away from Trindon Holliday and gave it to receiver Eric Decker. Holliday remained the kickoff returner.

“Just a little bit of a changeup,” Broncos coach John Fox said. “Eric’s a little bit of a rangier body, covers a little bit more ground.”

Decker was working on a sensational 47-yard punt return, breaking three tackles along the way when he tripped himself up in the open field.

“I guess it was that invisible fence again that got me,” said Decker, who also tripped in the open field after a long reception at San Diego last year. “I got a little excited and tripped myself, and I wish I could have that play back.”

Game-day roster moves. The Broncos’ seven inactive players: Ronnie Hillman, quarterback Zac Dysert, Carter, guard Chris Kuper, tight end Joel Dreessen, defensive end Derek Wolfe and defensive tackle Sione Fua.

Allen hot in Denver. Chargers wide receiver Keenan Allen had two touchdown catches in the San Diego regular-season win in Denver, and two more — both for 16 yards — Sunday. “I just think we came out flat and not how we wanted to,” he said. “We couldn’t capitalize in third downs coming out of the first half. We tried to make a turnaround, but it was obviously too little, too late.”

Footnotes. Britton Colquitt didn’t have a single punt for Denver. He did hold for Matt Prater’s three extra points and two field-goal attempts, so he at least officially got in the game. … Late in the third quarter, Prater had a 47-yard field-goal attempt hang up in the wind and float to the left. No good. It would have given Denver a 20-0 lead. … The Chargers lost linebacker Manti Te’o to a concussion in the first half.