SANTA CLARA, Calif. — 49ers coach Kyle Shanahan said Monday that decreasing All-Pro linebacker NaVorro Bowman’s playing time is the best way to keep him fresh.

Bowman, who’s made a career of playing every defensive snap, was sidelined by Shanahan’s coaching staff for the better part of three possessions Sunday in the overtime loss to the Colts.

“I do strongly believe keeping Bo as fresh as possible gives him the best chance to be successful – it gives our team the best chance,” Shanahan said. “Our defense has been averaging about 80 plays a game. And that’s a little too much for him, really all our linebackers.”

Bowman, 29, has been named an All-Pro each of the four seasons in which he’s started all 16 regular season games. But he missed the final 11 games last season with an Achilles tear. The injury came on the same left leg as his career-altering knee injury from the NFC title game that caused him to sit all of 2014.

Still, Bowman led San Francisco’s linebackers with 58 snaps played in Indianapolis. He’s been removed from games throughout the season in favor of safety Jaquiski Tartt when opponents are in long-yardage situations. The evolving style of play in the NFL generally favors speed against the passing game, rather than linebackers who do their best work defending the run between the tackles.

“I know that’s not something that any players like, but that’s the decision we feel. I think it will help him in the long run,” said Shanahan.

The 49ers fell to 0-5 against the Colts with their second straight overtime defeat. They became the second team in history to lose four consecutive games by 3 points or fewer, joining the Houston Oilers of 1994. San Francisco is one of three winless teams remaining joining the Giants and Browns.

Despite the rough start to his first season, Shanahan indicated he’s optimistic about his team staying competitive and won’t make sweeping changes in the coming weeks.

“Our guys have been in it and have a chance to win all these games. I was disappointed as anyone that they haven’t. I also know that we very easily could be 4-1,” he said. “I would never (make a change) just to do it, especially at this time. I always am going to try to do what I think gives us the best chance to win.”

Shanahan will have to consider a change in the starting lineup when Reuben Foster returns to practice Wednesday. The promising rookie linebacker, drafted 31st overall, has been out with a high ankle sprain suffered 11 snaps into the season opener.

Foster may be Bowman’s long-term replacement, although it’s likely they play together this season when both are fully healthy. Foster during the preseason stayed on the field in passing situations in which Bowman sat. Shanahan wouldn’t commit to Foster playing Sunday in Washington.

The 49ers on Monday waived undrafted rookie safety Lorenzo Jerome and claimed former Chargers safety Dexter McCoil. Jerome played 20 snaps Sunday. Safety Eric Reid is also expected to return to practice this week after sustaining a knee injury Week 2.