The NFL said following a detailed investigation and a hearing, Commissioner Roger Goodell determined the 49ers violated the league's anti-tampering policy by contacting the agent for Chicago linebacker Lance Briggs during the 2007 season without the Bears' permission.
The Bears leveled tampering charges against the 49ers, then re-signed Briggs at the beginning of this year's free-agency signing period.
"The 49ers organization respects commissioner Goodell's ruling today, however, we do disagree with it," 49ers General Manager Scot McCloughan said. "This was not a malicious act."
The Bears and 49ers will switch third-round selections in the 2008 draft. Chicago will have the seventh selection of the third round and San Francisco will have the 12th pick of the same round.