Rookie first-round pick Reuben Foster is set to take Bowman's starting spot, with the first-round pick poised to return from a high ankle sprain suffered in the season opener.
Despite recent injuries, Bowman has 38 tackles this year.
The report of the 49ers talking trade with teams comes on the heels of the 49ers deciding to sit Bowman for some series to keep him fresh.
"It became evident that going in different directions was best for both him and our team", Lynch said.More news: Palestinian rivals Fatah, Hamas sign pact
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).
"NaVorro gave his heart and soul to this team for the last eight years, and for that we are all extremely grateful", San Francisco general manager John Lynch said in a statement.
"Drew spoke to me on Monday night and indicated his frustration on behalf of NaVorro and I told him that I had talked with Kyle and his staff and that we were convicted, that we felt like this was the best thing for him, which in response Drew communicated that if that's the case NaVorro would prefer to be traded". He's signed through the 2019 season with a base salary of $6.75 million this year and $8.7 million next year, per Spotrac.
Bowman made three-straight Pro Bowls with Fangio as his coach from 2011-2013 before a knee injury forced him to miss all of 2014, Fangio's past year in San Francisco. However, he was not on the field much during the team's Week 5 loss to the Indianapolis Colts, even though he was not injured.
With Bowman gone, the 49ers basically discarded the last major piece of their team that reached Super Bowl XLVII. They have a very good defense, and their offense is doing enough to win some games.