"NaVorro gave his heart and soul to this team for the last eight years, and for that we are all extremely grateful," Lynch said in a statement. "During that time, NaVorro was a key component of one of the best teams in the league and his passion for the game allowed him to quickly become a favorite of our faithful fans.
"Thursday evening, Kyle and I met with NaVorro, and from our conversation it became evident that going in different directions was best for both him and our team. Although NaVorro may be moving on, he will always be looked at as one of the great players to wear the red and gold. We wish him and his family great success."
The 6-foot, 242-pound Bowman was originally selected by the 49ers in the third round of the 2010 NFL Draft out of Penn State.
The eight-year veteran earned First-Team All-Pro honors four times in his career (2011-13, 2015), as well as three trips to the Pro Bowl (2013-14, 2016). During his career, he has appeared in 89 games (74 starts) and registered 808 tackles, 12.5 sacks, four interceptions (returning one for a touchdown), seven forced fumbles, five fumble recoveries and 28 passes defensed. Bowman also led the team in tackles in four of the previous six seasons (2011-13, 2015).
Bowman missed the entire 2014 season after suffering a gruesome leg injury in the 2013 NFC Championship Game loss to the Seattle Seahawks.
Bowman leads the 49ers with 38 tackles this season in his return from an October 2016 Achilles' tear.
Shanahan was asked Monday about taking a look at younger players in an effort to build for the future.
"I think it's a fair question, especially when you're 0-5," Shanahan said. "But, I think my goal right now is I try to keep perspective ... so I don't want to sit here and just make a ton of changes and totally go that direction."
Bowman is making $6.75 million base salary this season as part of a four-year extension he signed last year under former general manager Trent Baalke. Bowman's salary-cap figure next year goes to $12 million, according to the San Jose Mercury News.
Bowman did not hide his displeasure after Sunday's 26-23 overtime loss to the Indianapolis Colts, upset over being replaced in favor of Brock Coyle for a couple of series.
"I don't know, man," Bowman told reporters Sunday about coming off the field. "We had a conversation and, I don't know -- they're doing what they want to do and, I don't know. I don't like it. No one likes coming out of the game, but I'm a team player."