Smith, whose role with the 49ers was assumed last season by rookie Patrick Willis, will bolster San Diego's inside linebackers group.
He spent seven seasons with the 49ers, and was their leading tackler from 2001-05. He's spent the last three years playing in a 3-4 defense, which is what the Chargers play.
Smith was drafted by the Washington Redskins in 1997 and played four seasons under Norv Turner, who is entering his second season as San Diego's head coach.
Neither general manager A.J. Smith nor Turner returned phone calls seeking comment.
Terms of the deal weren't available.
Smith, an 11-year pro who signed a three-year contract extension before the 2006 season, was due to make $3.28 million in base salary next season.
Willis, the NFL's defensive rookie of the year, took over Smith's role as the 49ers' defensive leader and top tackler.
Smith has long been one of the NFL's top unsung defensive players, annually racking up gaudy tackling statistics with little fanfare. He made at least 123 tackles in each of his first nine NFL seasons.
He was voted the 49ers' co-MVP in 2005, but missed two games in 2006 because of a strained eye muscle that limited his peripheral vision, eventually requiring surgery. He started 14 games and made 98 tackles last season, but his playing time decreased significantly in the final months of San Francisco's fifth straight losing campaign.