The girl's biological mother was also arrested for allegedly assisting her husband in the crime, they said.
Sagar Rathi (35) and his wife Asha were arrested by Sarkarwada police last night, after their neighbour in Gokul Nagar locality of the city rescued the little girl and lodged a complaint against the couple.
According to the complaint lodged by a woman neighbour of the couple, the step-father, who was a drunkard and worked as watchman at a building in Gokul Nagar, used to beat the girl and lock her in bathroom. He once also tried to suffocate the child by pushing her head down in a pail of water and also put chilly powder on her.
Sagar and his wife have been booked under relevant sections, including the Protection of Children from Sexual Offences Act, 2012.
The man had started physically torturing the girl after Asha delivered a baby five months back, police said, adding that further investigation was on.