The incident came to light at 11 AM yesterday, when a neighbour found the bodies of the two girls on a bed, while their parents were not at home.
The police were informed and from preliminary investigation it emerged that the girls were strangled to death while they were sleeping, said a police official.
Their father is a security guard and mother works at a nearby factory. Both had left for work in the wee hours yesterday.
A team was deployed and the youth, identified as Tahir Ali (28), an auto-rickshaw driver, was arrested late last night, DCO (East) B S Gurjar said.