Kaya Langmead was left with "red raw" skin after getting stuck to the seat at McDonald's in Exeter's High Street, her mother, Nicole Langmead, said.
Devon and Cornwall Police said the girls had "apologised to the victim's mother for the upset caused to her and her daughter".
Police said the case, which was treated as an assault, has since been closed.
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Ms Langmead said her daughter managed to free herself from the toilet seat, thought to have been covered in super-strong glue, but was in tears after the incident which was thought to have been a prank.
A police spokesman said: "Following injuries to a four-year-old girl at the McDonalds in Exeter High Street on New Year's Day, police identified two juvenile girls who were subsequently interviewed by police.
"The two girls immediately accepted what they had done, were sorry and have apologised to the victim's mother for the upset caused to her and her daughter.
"Devon and Cornwall Police have subsequently taken appropriate action against the offenders."
He added that Ms Langmead was "happy with the outcome".
McDonald's previously said staff swiftly offered medical help and contacted police "as soon as our restaurant team was made aware of this incident".
Two girls have apologised to a mother whose child was glued to a toilet in a fast food restaurant.