The wide receiver will move to the NFC West champions after reportedly refusing to take a pay-cut with the Ravens.
The side's quarterback told NFL.com: "Anquan was a great receiver for myself and for our football team for this whole organisation.
"It's sad to see a guy like that go, but at the same time you want what's best for him and you just wish him the best of luck.
"You lose a lot of things, you lose a leader, you lose that fire. Most importantly, you lose a really good player and a guy that's done it over and over again."
Boldin led the Ravens in receiving yards in 2012 and scored the opening touchdown of their Super Bowl win over the 49ers last month.