The move by the NFC West champions makes sure the team is compensated if Goldson - who had been set to become an unrestricted free agent March 13 - signs with another franchise.
"There are no immediate plans to sign the franchise tag," Goldson's representative, Ben Dogra of CAA Sports, said in a text message. "We will continue to speak with the 49ers."
General manager Trent Baalke said the team can still attempt to sign Goldson to a long-term deal but at least knows he is expected to be with the Niners again in 2012.
"Dashon has been a 49er since we selected him in the fourth round of the 2007 draft," Baalke said. "By using the franchise tag on Dashon, it affords us the opportunity to continue to work on a long-term contract with him, while also ensuring he will be a 49er for a sixth season, in 2012."
Negotiations with Smith are under way, with both sides making it clear they want to get something done. Dogra's group, with Tom Condon, also represents Smith.
He and cornerback Carlos Rogers shared the team lead with six interceptions - a career-best for Goldson, who was drafted out of Washington.
The franchise tag number for safeties is expected to be about $6.2 million next season.
If Goldson receives an offer from another team, the 49ers would have the right to match the offer. If they choose not to match the offer, San Francisco would receive two first-round draft choices as compensation. The franchise tender will provide Goldson with a one-year guaranteed contract equivalent to the average of the top five highest paid players at his position each year, over the last five seasons.