The toddler was with his Eritrean parents who were attending a baptism ceremony at a Catholic church in Wattwil on Saturday afternoon, cantonal police said.
Shortly after 2.30pm the parents of the boy noticed the absence of their son and alerted authorities.
Police immediately launched a search operation involving local fire fighters and the Rega emergency rescue helicopter service.
Searchers scoured the village centre of Wattwil on Sunday and began looking along the Chur River.
On Monday, teams with dogs and divers searched the Thur River again, discovering one of the boy's shoes in a meadow near the river, the Blick newspaper reported online, citing confirmation from a police spokesman.
Semere's father thought he was with the boy's mother, while the mother thought he was with her husband, Sinit Gebar, a 24-year-old woman whose son was baptized at Sunday's ceremony told the daily.
When last seen, the boy was wearing a brown sweater with pink stripes and brown trousers.