Samuel (hamstring) has been ruled out of Sunday's game in New England, Dan Graziano of ESPN.com reports.
Prior to his departure in the second half, Samuel had five catches (on five targets) for 65 yards and three carries for seven yards. After undergoing June surgery on a Jones fracture in his left foot and undergoing a recovery that extended into the regular season, he may be poised for another absence from the 49ers offense.