In turn the team signed former Colt safety Antoine Bethea to a four-year deal, as first reported by ESPN.
Beathea will turn 30 in July and has started every game for the Colts dating back to 2008 and started 14 games for the Super Bowl winning team as a rookie in 2006. The eight-year veteran made the Pro Bowl in 2007 and 2009.
Bethea's new deal is for four years and $23 million, as reported by the Associated Press, coming in slightly below Whitner's deal over the same duration for $28 million. Whitner was rated as the league's No. 6 safety while Bethea was No. 53 last season, according to Pro Football Focus.
The 49ers will turnover at least half of their starting secondary in 2014 after releasing Carlos Rogers, saving them $6.6 million in cap space. Corner Tarell Brown remains a free agent.
UPDATE: WEDNESDAY 3/12
Bethea will receive $6.5 million in guarantees, according to a source. Whitner will get a reported $13 million in guarantees from Cleveland.
While the average salaries differ by just $1.25 million each season, the 49ers afforded themselves far more flexibility going forward by giving Bethea half of the guaranteed dollars Whitner received from the Browns.
Follow Editor in Chief Chris Biderman on Twitter.