The accused, identified as 35-year-old Rakesh Mishra, a motor mechanic, has been arrested.
"The man had been staying in the victims' house in Shahbad Dairy area in north Delhi for the past one year and raped the sisters aged 13 and 11 years several times," a senior police officer told IANS.
On Wednesday night, the elder sister revealed the situation to a neighbour, who, in turn, informed police.
A medical examination, conducted on the two girls, confirmed rape. Police then brought them before the child welfare committee.
Police said Mishra, who came from Uttar Pradesh's Kushinagar, is married and has five children. He was having illicit relations with the victims' mother, who works as a maid in several houses, since the last one year.
"We are verifying whether their mother knew about the assault. Two separate cases of rape have been registered against the accused," the officer said.