Reto Felder, a goalkeeper who plays for Muri in the Swiss fourth division, says in the Blick daily newspaper he first thought his drink was warmed by the sun. He called the prank "crude and disgraceful."
Fans in the crowd of about 500 reportedly persuaded a ball boy to pass them the bottle.
Muri lost at Baden 3-2 on Saturday.
Baden president Thomi Braem, who promised to investigate, says fans "should realize they have again done great damage (to the club)."
Muri coach Beat Hubeli says the incident was "the lowest of the low."