SANTA CLARA, Calif. — Linebacker Malcolm Smith, a standout in the 49ers’ spring practices who had been playing next to NaVorro Bowman, is finished for the season after tearing a pectoral muscle in Saturday’s practice.

Kyle Shanahan hinted at that development, which was later reported by the NFL Network.

The 49ers signed Smith, 28, to a five-year, $26.5 million free-agent deal in March. They pursued him because of his familiarity with the defense and because he’s one of the fastest linebackers in the league, a trait he showed off in the spring. Smith and defensive coordinator Robert Saleh were in Seattle together, and Smith caught the interception that ended the 49ers’ comeback bid against the Seahawks in the 2013 NFC championship game.

His absence seems to clear a path for first-round draft pick Reuben Foster, who’s been practicing at the same weak-side linebacker spot at which Smith plays, but with the second-team defense. Foster has made a number of big plays in recent practices, although coaches have been cautious with their praise.

“Reuben, he has a lot of flash plays,” Saleh said on Wednesday. “The best way I can explain with Reuben is he’ll get his opportunity when he absolutely, absolutely deserves it.”

When Smith left Saturday’s practice, Ray-Ray Armstrong filled in with the first-team defense and Foster remained with the second-string unit.

“That would be a big (injury) for us, just because we’ve been getting so many reps together, jelling together,” Bowman said of Smith before his diagnosis was known.

Bowman said that Armstrong, a one-time safety, is good in coverage while Foster is excellent at attacking the line of scrimmage. He said either could step in, but didn’t want it to be at Smith’s expense. “Let’s hope not,” he said.

Meanwhile, another would-be 49ers starter, guard Joshua Garnett, also missed practice and may have to have surgery to “clean up” his left knee, Shanahan said.

Garnett, who was a first-round draft pick a year ago, will miss time, but the 49ers are holding out hope that he won’t be lost for the season. Zane Beadles filled in for him at left guard with the first-string offense on Saturday.