Goal umpire Steven Piperno suffered a cut to the back of the head and had to be replaced on the field by a reserve during the second quarter of the round-24 match at Marvel Stadium on Sunday.
The incident took place in front of the Carlton cheer squad, with a significant portion of Blues fans incensed by a one-sided free-kick count at the time.
St Kilda appeared to have the rub of the green through the first half of a contest Carlton need to win to guarantee their spot in the finals.
A loss would leave the door open for Fremantle to pinch eighth spot from the Blues.
Security guards were spotted talking to crowd members soon after the incident, seemingly trying to discover who had thrown the bottle.
An AFL spokesperson confirmed to AAP the league would investigate.
In the television broadcast, Geelong great Joel Selwood and fellow AFL premiership player Dale Thomas agreed the perpetrator would not be welcome back at the football.
"That is just an absolute disgrace," Seven commentator Brian Taylor added.
"There is just no room for that anywhere in any of our games."
St Kilda led the free-kick count 12-1 during the second quarter and 12-3 at half-time.
A section of Carlton fans broke into chants of "Bulls**t! Bulls**t!" during the second term.
