The head coach didn't show confidence that the fullback would be returning anytime soon.
“It doesn't look good," Harbaugh said. "It looks like he has an injury to his scapula. I won't say anything officially, but it doesn't look good."
Harbaugh said the 49ers will be looking at options which include Owen Marecic, who is planning to come in presumably for a physical. Marecic was a former Stanford player under Harbaugh and briefly spent time with the team in September before being cut.
The loss of Miller would bring the question of who becomes the team's fullback. Anthony Dixon and Demarcus Dobbs have both spent time at the FB position on offense in the past. If his injury is significant, Miller would most likely go on the injured reserve and Marecic would take his place on the 53-man roster.
A former seventh round draft pick in 2011, Miller has been nothing but consistent for the 49ers offense and even special teams. He helped contribute to the resurgence of Frank Gore with two seasons of 1,200 rushing yards or more in 2011 and 2012. Gore reached the 1,000 yard rushing mark for the seventh time in his career.
Harbaugh said the team will be looking at all options, but he felt doubtful that he will return with an injured scapula (shoulder blade). He talked about how he contributes everywhere on the field.
"He does so many things in protection and the run game," Harbaugh said. "From being part of the receiving end of the backfield, He's a multi-talent used player. From special teams and two or three phases, it's a loss."