Brazilian soccer's disciplinary tribunal ordered the club to play next month's match against Gremio at least 150 kilometres from their Vila Belmiro stadium following the incidents during a 1-1 draw with Corinthians in October.
Santos representative Mario Mello said the punishment was harsh.
'Santos were punished for firecrackers which were thrown by Corinthians supporters' he told reporters.
Santos are second in the table two points behind Atletico Paranaense with five games to play.
The tribunal has handed out a number of bans in the last month in an attempt to cut down on missile-throwing.
Four of last weekend's 12 first division games were subject to home bans with Gremio Juventude Santos and Atletico Mineiro forced to use alternative venues.
Bottom of the table Gremio have been the hardest hit having been banned from the Olimpico stadium plus their first choice alternative in Pelotas where fans also threw missiles on to the pitch during a 3-2 defeat by Palmeiras.