John Elway, a former NFL quarterback and current head of football operations for the Broncos, was among the Denver officials who travelled to North Carolina to audition Manning, according to the league's website.
The 49ers joined the Broncos and Tennessee Titans as teams looking to land Manning's services while the Miami Dolphins and Arizona Cardinals are out of the mix, according to ESPN.
The four-time NFL Most Valuable Player was cut last week by the Indianapolis Colts, who have decided to rebuild after a 2-14 season without the 35-year-old Manning, who missed the entire 2011 campaign after having neck surgery.
Manning was expected to decide where to resume his career when the free-agent signing period began on Tuesday, but the process has been extended as he works out for his suitors.
The quarterback worked out for San Francisco Tuesday at Duke University in North Carolina, where 49ers coach Jim Harbaugh and offensive coordinator Greg Roman observed a passing session, ESPN reported. The team brought in a doctor the following day to administer a physical exam.
Alex Smith, who quarterbacked the 49ers to within one win of a Super Bowl appearance last season, recently became a free agent despite reports that he had been close to signing a three-year deal with the team.
Manning, an 11-time Pro Bowler, was also expected to work out for the Titans in the next few days before making a decision on where to resume his career.