SHO Loni border area Dinesh Yadav said the alleged incident happened when the house owner's, Sanjoo (29), family had gone outstation.
Sanjoo called his tenant's son to sleep with him and as the teenager was friendly with the landlord, he agreed, Yadav said.
He said the landlord allegedly indulged in the offence post-midnight and when the boy cried for help his parents came and informed the police.
Police reached the spot and sent the boy for medical examination. Sanjoo has been sent to jail under section 377 of the IPC, the officer added.