Smith is on indefinite leave from the team for treatment for substance abuse at an in-patient rehabilitation facility after a DUI arrest in September.
He is also facing three felony charges of possessing illegal assault weapons stemming from a 2012 party at his home.
The 49ers believe the 24-year-old has a significant amount of work to do to turn his life around.
Even if Smith does return to the team this season, the 49ers realize he still may face a suspension from the NFL and is one incident away from a one-year ban. But discipline from the league could be pushed back to next season.
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The NFL Players Association wants the NFL to investigate Tampa Bay Buccaneers coach Greg Schiano and his possible role in leaking information about former quarterback Josh Freeman's status in the league's substance-abuse program.
USA Today reported Saturday the union asked the NFL for help to form a joint investigation so union officers could question Schiano and other Buccaneers officials.
Buccaneers cornerback Johnthan Banks played Sunday against the Philadelphia Eagles, despite being diagnosed with MRSA last week.
Guard Carl Nicks, who had a recurrence of the infection, did not play.
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New England Patriots tight end Rob Gronkowski did not play in Sunday's game against the New Orleans Saints.
Gronkowski practiced all week, but the team did not clear him to play. He is recovering from multiple back and forearm surgeries.
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Houston Texans quarterback Matt Schaub suffered a right leg injury during the third quarter of Sunday's game against the St. Louis Rams.
Schaub's lower leg twisted underneath him on a sack by Rams defensive end Chris Long. Schaub was able to walk to the sideline but was replaced by backup T.J. Yates.
Houston fans cheered when the embattled Schaub was hurt and Yates trotted onto the field to take over.
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Green Bay Packers wide receivers James Jones and Randall Cobb sustained leg injuries in the first half of Sunday's game against the Baltimore Ravens.
Jones injured his left knee in the first quarter while blocking for running back Eddie Lacy. He did not return.
Cobb hurt his right knee after he caught a 15-yard pass on a drive near the end of the first half. He left on a cart.