Police have slapped Protection of Children from Sexual Offences Act against the culprit.
The six-year-old girl and her four-year-old brother were strangled and dumped along a ghat section on Goa-Karnataka border, but both survived.
Their parents had been murdered before that.
Osban Fernandes and Ramesh Bhagwe have been arrested for murdering the couple Shivaji Nayak and Sujata Nayak and trying to kill the two children.
A senior police official today said Bhagwe had confessed to have sexually abused the girl in the car on Monday midnight.
She was dumped two km from the border, inside Karnataka, but a man found her wandering and alerted the police.
Sujata's relatives today arrived from Chikodi village in Karnataka to take the custody of the children and the dead bodies. Shivaji hails from Gadhinglaj, Maharashtra.
Both the victims were working as labourers with Fernandes at Merces village near here.
Fernandes and Bhagwe allegedly killed Shivaji over a petty brawl on last Saturday night, and later killed his wife.