The 49ers are expected to turn to first-round draft pick Reuben Foster as Bowman's replacement.
"It became evident that going in different directions was best for both him and our team", Lynch said.
"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".
In five games this season, the 6-foot, 242-pound linebacker has recorded 38 tackles and one tackle for a loss. He's certainly still capable of being a defensive contributor and could see a boost in production if he lands on a team that gives him more field time. He may never receive the recognition he merits as a result of his injuries, but he will forever be remembered by the 49ers as a cornerstone of a team that, but for a few bounces of the ball, could have celebrated three successive Super Bowl titles.
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.
Bowman returned the following year and led the National Football League in tackles. But another injury past year to his Achilles tendon cost him 12 games, and he's been noticeably slower to react in the passing game this season. He now leads the team in tackles, but his lateral quickness and his ability to cover opposing pass catchers appears to have been compromised by his recent injuries. Foster likely would have eaten into Bowman's snaps as the season wore on, Lynch said. San Francisco also has Ray-Ray Armstrong playing well at the Will linebacker spot and the injured Malcolm Smith is locked down to a lucrative long-term deal.