Coach Mike Nolan said Trent Dilfer would make his sixth start of the season Sunday against Minnesota in the place of Smith, who was not made available for comment following his brief prepractice workout.
A team spokesman said that the 49ers medical staff would assess Smith's condition today, and his throwing regimen could gradually increase in the coming days. If Smith continues to have problems, season-ending surgery remains a possibility.
"It's going to be a touchy-feeling thing. We're just going to see how he does," Nolan said of Smith's first throwing session since Nov.18.
At this point in Smith's rehabilitation, Nolan said he could put no timetable on his return. Because of the lingering nature of Smith's injuries, Nolan also remains wary of giving him the go-ahead, even if he's eventually cleared by the team's medical staff.
"As we learned once before, that's not the total ticket," Nolan said. "You still have to ask the player, don't you? We'll re-evaluate at that time and see where we stand."
Smith suffered a third-degree shoulder separation Sept.30 against Seattle when he was sacked and slammed into the ground by defensive tackle Rocky Bernard. He returned a month later but played ineffectively in three games.
During a news conference prior to practice, Nolan insisted that he and Smith have patched things up and their communication has gotten better.
"I think our relationship is fine," Nolan said. "I think a lot more was made of that than had to be. We do communicate. Was there a little glitch at one point? Yes, but it was both sides. You've got to tell me if it's hurting. Don't surprise me with it. I can't read your mind. But outside of that, there's no issues there."
Nolan said there were no ulterior motives in his refusal to endorse Smith as the team's starting quarterback for the rest of this season and beyond, along with his strong public backing of Dilfer as the quarterback giving the team its best chance to win.
"When everyone's healthy, everybody's playing well, he's the guy," Nolan said of Smith. "But that's not the way it is today.
"I'd like to think he's the quarterback of the future, but he's got to get healthy and get back on the field. With all the talk about his shoulder, this and that, heck, I'm living in today. I don't have time to go there. We've got Minnesota this week."
DEATH IN THE FAMILY: Defensive coordinator Greg Manusky was with family in Pennsylvania following the death earlier this week of his father, Frank Manusky, who was 72. In Manusky's absence, Nolan ran the defense at Wednesday's practice. Manusky was expected to return in time for today's practice but was expected to leave again to attend his father's funeral, scheduled for Saturday in Wilkes Barre.
Nolan said he and Manusky have already discussed the defensive plan for the Vikings game and plan to visit about it again upon his return. Nolan said he'll decide later whether he or Manusky calls the plays on Sunday.
"Calling the game is Greg's responsibility," Nolan said. "But with what he is going through, I'm not going to put him in a situation where he's not prepared and our team is not prepared."
EXTRA POINTS: Nolan would not say whether the issue of his job security had come up in his recent conversations with owners John and Denise York. "I talk to them all the time, but I don't ask them every day if they love me," Nolan said. The Yorks are said to be leaning toward bringing Nolan back for a fourth season. ... Cornerback Marcus Hudson will miss a second consecutive game with a sprain of the posterior cruciate ligament. Running back Frank Gore (ankle) took part in practice on a limited basis. Linebacker Derek Smith (groin) and cornerbacks Shawntae Spencer (quadriceps) and Donald Strickland (knee) did not practice.