SANTA CLARA — Rookie quarterback B.J. Daniels and fullback Owen Marecic were waived Tuesday by the 49ers, who filled one of those roster spots by signing former Patriots linebacker Jermaine Cunningham.

The other vacant slot reportedly will be filled by former Cardinals quarterback John Skelton, a source told the Sacramento Bee. Skelton’s agent, Neil Schwartz, referred inquiries to the 49ers regarding that potential signing. Skelton worked out for the 49ers on Sept. 3, and he auditioned Tuesday with the Tennessee Titans, according to The Tennesseean.

Daniels, a seventh-round pick out of the South Florida, was not active for any game as the 49ers got off to a 2-2 start. Marecic, a former Stanford star under coach Jim Harbaugh, was signed two weeks ago but did not play in either game since then.

Cunningham (6-foot-3, 255 pounds) was a 2010 second-round draft pick by the Patriots, who released him at the end of this year’s training camp. He served a four-game suspension late last season for violating the league’s policy on performance-enhancing substances. Cunningham started 11 games as rookie and has only 3½ sacks through 36 career games.

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