Jacobs on Saturday said via Instagram that he is "on this team rotting away" while referring to his first season with the Niners as his "worst" yet during an eight-year career that included seven with the New York Giants.
In recent days, he posted a series of photos of himself playing for the Giants -- and even a picture of his two Super Bowl championship rings, side by side.
"I am on this team rotting away so why would I wanna put any pics up of anything that say niners," Jacobs said. "This is by far the worst year I ever had, I'll tell you like I told plenty others."
The 30-year-old Jacobs has five carries for 7 yards while being active for only two games with the NFC West-leading Niners (9-3-1), who beat the Miami Dolphins 27-13 on Sunday.
On Twitter later, Jacobs said: "I don't understand why people are angry at me because I wanna do what I am paid to do, I am a competitive person, I think people should be mad if I didn't wanna play. ... As for all of my Instagram photos I don't have any niner pics, if you'll find me some pics I'll put them up."
Jacobs, hampered by a knee injury earlier this season, spends approximately 20 minutes before games punching the goal-post padding. He has said it is his way of dealing with the situation.
When asked after Sunday's game about Jacobs' comments, Harbaugh only said, "I have no comment for that."
Last month, Jacobs posted advice on Twitter with a reference to never working "in a place where you hate your boss so much, you should always be happy at work" with a hash tag of "YouLiveAndYouLearn."
His post came the same day Harbaugh was hospitalized for a minor procedure for an irregular heartbeat.
Jacobs then said people shouldn't "assume" his remarks were football-related, then followed up with more tweets -- including one reading "football is not my life, people" and another saying, "Have you ever been in a spot and you wonder why are you there."
Later, he posted that his tweets referred to his brother's boss, who makes "him feel like he is the best thing since slice bread but when the budget is shot he is the first one get laid off, same with two other people I know."
The 30-year-old Jacobs ran for 571 yards and seven touchdowns last season as a backup to Ahmad Bradshaw. He is the fourth-leading rusher in franchise history with 4,849 yards, but saw his role diminish with the emergence of Bradshaw and became increasingly disgruntled.