The person spoke on condition of anonymity because no announcement had been made. Smith was expected to sign within the day. Smith's new deal, which was all but done late Tuesday, can pay him up to $33 million.

On Tuesday, Peyton Manning was formally introduced in Denver after the 49ers pursued the four-time NFL MVP. Coach Jim Harbaugh worked out Manning at Duke last week.

The 27-year-old Smith met with Miami on Sunday but ultimately decided to stay put with the storied franchise that drafted him first overall in 2005.

Smith had a breakthrough season last year, throwing for 3,150 yards and 17 touchdowns to help San Francisco reach the NFC title game.

Both sides made it clear after the Niners' 20-17 overtime loss to the eventual Super Bowl champion New York Giants in the NFC championship game that they planned to work out a new deal.

It just took a little while longer than expected after Manning briefly entered the picture.

Smith and Harbaugh built a strong working relationship in a matter of months, and Smith told the South Florida Sun-Sentinel on Sunday that he understood the business side of the NFL. So, perhaps it won't take long for Harbaugh and Smith to get over San Francisco's weeklong courting of Manning.

"It's a very strong relationship," Harbaugh told reporters while leaving team headquarters Tuesday, noting nothing had changed in Smith being "our guy."

Last spring, Harbaugh handed over his playbook to Smith during a brief lifting of the lockout -- a show of confidence in the QB even though he wasn't under contract. Smith wound up re-signing for $4.9 million, then earned a $1 million bonus for making the playoffs as the 49ers ended an eight-year stretch without a postseason berth or winning record.

Now, he is getting some job security and a nice raise to boot.

"Oh, I'm excited," tight end Vernon Davis said in a text message. "I'm glad. Alex deserves all good things that come his way."

49ers CEO Jed York had said the team's three-year offer still stood despite the pursuit of Manning, and it was just up to Smith to sign.

"I don't think there will be any bad blood because he went to Miami for an interview," former 49ers running back great Roger Craig said Tuesday. "That's part of the process, it's the nature of the beast. He has to do what's best for him and his family. I'm pretty sure the 49ers are going to work something out. Players love him, fans love him. I love him.

"I think Alex wants to get this put to bed so he can focus on having a great year, an All-Pro year this year," Craig said. "He doesn't want this dark cloud over him. It's really his time, and he understands the business. He knows it's a good situation."

Long booed by his home fans at Candlestick Park, Smith had only five interceptions last year as San Francisco went 13-3 to win its first division title since 2002. That was a remarkable turnaround under first-year coach and 15-year NFL quarterback Harbaugh -- the NFL coach of the year -- who declared his confidence in Smith as a winner from Day 1 when Harbaugh was hired away from Stanford in January 2011.