The 49ers agreed to a one-year contract with former Giants running back Brandon Jacobs, a league source said Wednesday. Jacobs is the second former Giant to join the 49ers this offseason, following receiver Mario Manningham, who signed a two-year contract last week.

The 49ers signed quarterback Josh Johnson and return specialist Ted Ginn Jr. on Thursday. Johnson, an Oakland native and former Buccaneers backup, signed a two-year deal while Ginn Jr. signed a one-year contract.

The 49ers have officially added a player who helped deny them a trip to the Super Bowl, reaching a two-year deal with wide receiver Mario Manningham. The team announced the deal on Thursday, five days after Manningham's agent, Drew Rosenhaus, said the sides agreed to terms.

The 49ers have re-signed Alex Smith after they tried to court Peyton Manning and Smith negotiated with the Dolphins. Smith officially signed his three-year deal with the 49ers on Wednesday. It will pay him $8 million per season with $16.5 million guaranteed, according to a source.

There is no bad blood between Jim Harbaugh and Alex Smith after the 49ers pursued signing Peyton Manning, and Smith negotiated with the Dolphins. "It's been good -- strong relationship, as always," Harbaugh said. "It's a very strong relationship." It has been reported that the 49ers and Smith have agreed to terms on a new contract. "I always have a good policy, based on experience, that it's never wise, never benefits anybody concerned to discuss negotiations and contracts in the media," Harbaugh said. "We're in a negotiating time. We're in a free-agent period. We're in a contract talk. All these questions are about negotiations." Smith helped lead San Francisco to the NFC Championship Game and the team planned to re-sign him, but they courted Manning when he hit the open market. As reports surfaced that the 49ers met with Manning last week, Smith paid a visit to the Dolphins, who are still potentially in need of a quarterback.

While Josh Johnson has been a backup plan for the 49ers if they were unable to sign Alex Smith, his agent has scheduled a visit with the Redskins. Johnson was a fifth round pick out of San Diego by the Buccaneers in 2008 and played under Jim Harbaugh.

Alex Smith and the 49ers have agreed to a new three-year contract worth approximately $8 million per season. Smith earned $4.9 million in base salary in 2011. San Francisco also explored signing Peyton Manning before returning to the table with Smith.

Following Peyton Manning's agreement to terms with Denver, the 49ers have resumed their attempts to re-sign Alex Smith. San Francisco restarted talks with Smith on Monday, a day after he visited with Miami. Smith had been hoping for a stronger commitment than the three-year, $24 million offer from the 49ers that included some $10 million guaranteed. "We have a contract on the table, and it's up to him," 49ers CEO Jed York said. "We'd like for him to be here, and we'll see where it goes."

Peyton Manning's final three choices are the Broncos, 49ers and Titans. Insiders have conflicting opinions on which team Manning prefers. "His brain tells him San Francisco," said one source. "His heart tells him Denver.''

According to league sources, the Dolphins and Alex Smith are in negotiations on a contract. The assumption was that Smith would re-sign with the 49ers, but he has flirted with Miami ever since San Francisco was revealed to be pursuing Peyton Manning. Smith visited with the Dolphins over the weekend. Manning reportedly turned down Miami and they lost Matt Flynn, who joined the Seahawks. The two sides are believed to be talking about a multi-year deal worth about $8 million annually.