Manningham was beginning to get more involved in the offense following the quarterback change as Colin Kaepernick assumed the duties as starting signal caller, so the injury is especially devastating in his case as he nurses a shoulder ailment. Cornerback Tarell Brown also did not practice due to a hamstring injury.
Kicker David Akers (pelvis), cornerback Chris Culliver (illness) and linebacker Aldon Smith (shoulder) were each limited.
The rest of the 49ers injury report is as follows, and included a list of six players who turned in a full session:
LB NaVorro Bowman, LB, shoulder
LB Tavares Gooden, knee, elbow
RB Frank Gore, wrist
G Mike Iupati, shoulder
CB Carlos Rogers, knee
LB Patrick Willis, shoulder
The 49ers will host the Dolphins on Sunday at 1:05 p.m. PT at Candlestick Park.