SANTA CLARA — The 49ers suspended running back Brandon Jacobs for the remainder of the regular season Monday, seemingly ending a relationship that never quite meshed.

Jacobs often voiced frustration the past two months over his near-invisible role. In his latest social-media rant, Jacobs remarked last weekend that he was “rotting away” with the 49ers in what’s been “by far the worst year I’ve ever had.”

Jacobs, an eighth-year veteran, basically has been the 49ers’ fourth-string running back this season, appearing in only the two games that preceded Sunday’s 27-13 win over Miami. He had five carries for 7 yards.

The NFC West-leading 49ers (9-3-1) announced his suspension in a news release without further details.

General manager Trent Baalke said he had an “amicable” meeting with Jacobs on Monday afternoon.

“It comes down to the team and making the best decisions we can for the team,” Baalke said on his weekly radio show on 95.7 The Game. “We’ll leave it at that. But the discussion was amicable. We’ll leave the details of it in-house.”

Two hours before the 49ers sent word of Jacobs’ suspension, coach Jim Harbaugh was asked if Jacobs was still part of the team, to which Harbaugh replied: “I’ll go with the Fifth Amendment on that. No comment.”

Jacobs tweeted Monday night: “Thank you all for all your support, I am doing wonderful it’s not a big deal things happen, I am strong enough to get through this, again thank all of you for your support. #IWILLBEBACK.”

USA Today reported that Jacobs will file a grievance in hopes of getting reinstated, retaining his lost wages or gaining his release.

The 49ers signed Jacobs in the offseason to back up Frank Gore and perhaps be a short-yardage specialist. An Aug. 18 knee injury shelved Jacobs for nearly two months before he was able to fully practice.

Jacobs’ suspension will cost him approximately $168,000, according to ESPN’s Andrew Brandt, who reported that Jacobs’ one-year deal in April featured a $950,000 base salary and a $150,000 signing bonus.

Despite his inactivity, Jacobs’ value increased in recent weeks, a result of Kendall Hunter’s season-ending Achilles tear at New Orleans on Nov. 25.

Jacobs, had he been released instead of suspended, might have attracted interest from upcoming 49ers opponents or potential playoff foes.

Jacobs came to the 49ers after winning his second Super Bowl in seven seasons with the New York Giants, who are thin on running backs. Jacobs owns the Giants’ franchise record for rushing touchdowns (56).

In his Giants’ finale, Jacobs had nine carries for 37 yards in their 21-17 win over the New England Patriots in Super Bowl XLVI. In an interesting twist, the Patriots are the 49ers’ opponent this Sunday night.

Harbaugh and the 49ers have a precedent of distancing themselves from disgruntled veterans. Nearly a year ago, wide receiver Braylon Edwards got cut before their 2011 regular-season finale, even though he provided depth on a weak receiving corps.

Jacobs first voiced frustration with his role before the 49ers’ Oct. 14 game against the Giants, who won that contest 26-3 in a rematch of last season’s NFC Championship game. Jacobs told USA Today back then: “I’ve learned over the years when you open your mouth and say certain things, it hurts you, so I’m just going to shut up and keep working.”

Jacobs relayed a message through his Twitter account Saturday, explaining that his frustration stems from his competitiveness and that people shouldn’t hold that against him.

For more on the 49ers, see Cam Inman’s Hot Read blog at blogs.mercurynews.com/49ers. Follow him on Twitter at twitter.com/CamInman.