In a statement released by the league Monday, Goodell also said the teams will switch picks in the third round of the April 26-27 draft. Chicago, which had the 12th pick, will get San Francisco's seventh pick and the 49ers will get Chicago's choice.
Goodell said the 49ers violated the NFL's anti-tampering policy by contacting Briggs' agent, Drew Rosenhaus, about his client during the 2007 season.
"The 49ers organization respects Commissioner Goodell's ruling today, however we do disagree with it," 49ers general manager Scot McCloughan said in a statement. "This was not a malicious act; we believe that our intent was within the NFL guidelines. Going forward, we will take the necessary steps to ensure we are in compliance with the NFL's interpretation."
Briggs, an all-Pro in 2007, had been designated as Chicago's franchise player, signing a one-year tender that meant he could not leave the Bears.
He had been expected to leave as a free agent after last season but instead re-signed with Chicago for $36 million over six years. Briggs will earn $21.6 million in the first three years of the deal and $13 million of the contract is guaranteed.
"We are appreciative of the efforts of the league office on this matter and support the commissioner's decision," Bears president and CEO Ted Phillips said in a statement.
There had been reports of contact between the 49ers and Rosenhaus last season, and the Bears filed a tampering charge with the NFL. Goodell said both teams cooperated with his investigation into the allegations.