The 49ers announced the decision late Monday night after Smith's latest consultation with team doctors and Dr. James Andrews over the separated right shoulder that has bedeviled him for nearly two months. Smith will be placed on injured reserve this week.
San Francisco also expects to be without backup Trent Dilfer for Saturday's home game against Cincinnati after Dilfer sustained a concussion in Sunday's 27-7 loss to Minnesota.
Smith was sacked by Seattle's Rocky Bernard on the third play of a loss to the Seahawks on Sept. 30, and he was never the same. He sat out two games with the injury, then returned for an ugly three-game stint before the 49ers removed him from the lineup for the last four games when he complained of a still-sore shoulder and an aching forearm.
Smith completed just 48.7 percent of his passes for 914 yards, two touchdowns and four interceptions this season, struggling along with the rest of the NFL's lowest-ranked offense. His passer rating of 57.2 is the second-lowest among all quarterbacks who qualify for league statistics -- only better than teammate Trent Dilfer's 55.1.
The lingering injury increased tensions on the 49ers (3-10) during a hugely disappointing season for a team that began the year with playoff aspirations.
San Francisco coach Mike Nolan had a lengthy public disagreement with Smith and Tom Condon, Smith's powerful agent, over the team's handling of Smith's injury. Nolan insisted the 49ers proceeded according to their medical staff's recommendations and Smith's feelings, while Smith and Condon intimated Nolan hadn't understood the quarterback's concerns.
Smith rested his arm for two weeks after a poor performance at Seattle last month, then returned to a schedule of light throwing as the 49ers attempted to avoid surgery.
Smith was replaced by Dilfer, the 14th-year pro who has started six games this season. But Dilfer was taken to a hospital after a hard hit from Minnesota's Charles Gordon shortly before halftime.
Dilfer was released later Sunday, but Nolan declared him doubtful for the Niners' next game. Dilfer declined comment as he left the 49ers' training complex Monday, saying, "I can barely think, let alone talk."
"That kind of stuff always makes you think," Smith said of Dilfer's injury. "You want to be there for your teammates, but the past couple of weeks for me have been about safety and whether there's going to be any long-term damage."
San Francisco's league-worst offense and passing game have been so pathetic that Hill's effort against Minnesota produced the club's best passer rating of the season: 106.9, or nearly twice as good as the season numbers for Smith (57.2) or Dilfer (55.1).
Hill is playing with a bandage on the dislocated index finger of his throwing hand, which swells up after practices and games. Despite the solid numbers, he led just one scoring drive and wasn't overly impressed with the game tape of his first real action.
"Some things made me want to throw up, and on some things the execution was poor, but the results were good," said Hill. "If I am the guy this week, and I'm getting the reps in practice, I look forward to that challenge."
The 49ers also hope to sign a veteran quarterback Tuesday. Drew Olson, a practice squad member who joined the club just two weeks ago, is the only other quarterback on the roster -- not counting Michael Robinson, the star Penn State quarterback who's a kick returner and a running back for San Francisco.
Copyright 2007 by The Associated Press