SANTA CLARA, Calif. >> Quarterback Colin Kaepernick was placed on season-ending injured reserve by San Francisco on Saturday with a left shoulder injury, possibly signaling an end to his time with the 49ers just three seasons after he led them to a Super Bowl.

Kaepernick began the week coming off the team’s bye with soreness in his non-throwing shoulder and he brought it to the attention of the medical staff Monday. He received treatment throughout the week, but was listed as a full participant in practice.

He was listed as probable Friday to be available if needed for Sunday’s game at Seattle as the backup to promoted starter Blaine Gabbert.

But after the team submitted the injury report, Kaepernick returned to the training staff Friday following practice and said the shoulder wasn’t making any progress and then asked about his options. Surgery was considered a real possibility.

The 28-year-old Kaepernick’s $11.9 million 2016 contract would become fully guaranteed for injury if he’s still on the roster on April 1.

Because of that, many already figured Kaepernick’s time with the Niners (3-6) might be done in what so far has been a forgettable season.

Kaepernick’s time could be over with the franchise that drafted him in the second round out of Nevada in 2011.

He took over the starting job from Alex Smith in November 2012 and immediately showed the dynamic player he could be with his strong arm and quick legs — including that quarterback-record 181 yards rushing in a playoff win against Green Bay on the way to the Super Bowl.

Yet that guy never came to life this season, instead making more mistakes than memorable plays.

Gabbert took over for the benched Kaepernick against Atlanta on Nov. 8 and led the team to a 17-16 win, then coach Jim Tomsula said Gabbert would keep the starting job at least for another game this week against the rival Seahawks.

But the first-year coach hadn’t publicly ruled out Kaepernick returning at some point.

“I’m not into comparing the two guys,” Tomsula said this week. “I won’t compare the two guys, but Blaine right now is doing a good job for us and did a nice job last week. He’s been here for two years, so it’s a guy we know and he’s busting his tail.”

Initially when making the quarterback change, Tomsula said he wanted Kaepernick to “step back and breathe and look at things through a different lens.”

To that, Kaepernick said, “I’m not out of breath, so I don’t understand that reference.”

On Oct. 22, the 49ers managed just 142 total yards in a 20-3 home loss to Seattle, fewer than the 164 they had on Thanksgiving last year and their worst total since 133 yards against the Vikings on Nov. 5, 2006.

Kaepernick dropped to 1-6 in seven starts against the Seahawks with three touchdown passes to nine interceptions and 24 sacks, including the NFC championship game loss in January 2014.

The 49ers have lost four in a row to Seattle and six of seven, held to single digits in their past three defeats with just one touchdown while getting outscored 56-13.

San Francisco moved quarterback Dylan Thompson from the practice squad to the active roster to back up Gabbert.

Kaepernick’s agent didn’t immediately return messages Saturday.