Henry also used a hot pressing iron to burn his wife, Mercy, and stabbed her repeatedly in order to force her to confess to the allegation.
A police source said 40-year-old Henry had been suspecting that his wife was having an amorous relationship with his father for a while.
Our correspondent learnt that on Easter Sunday around 2am, Mercy turned down her husband's request for sex resulting in an argument between the couple.
A reliable police source told PUNCH Metro, "Henry and his wife live together in a room with their only child at 3, Lambe Street, Ago Palace Way, Lagos.
"The suspect had been suspicious of his wife's movement and on that very day, he came back home late in the evening and was ironing his customers' clothes on the floor while his wife and son were on the bed.
"His wife and son were both naked because the room was poorly ventilated. Henry then told his wife he wanted to have sex with her but she refused.
"Henry was infuriated by her refusal and saw it as a confirmation of his suspicion. He grabbed the pressing iron and started inflicting burns all over Mercy's body, including her private part, asking her to confess."
PUNCH Metro learnt that the suspect immediately grabbed his son and fled. However, the corpse of his son was later found in the compound.
Our correspondent learnt that the landlord, Mr. Amao Lateef, immediately informed the Okota Police Division and Mercy was rushed to a nearby hospital where she has been receiving treatment.
According to sources at the Okota Police Division, the couple who have been married for two years, had a history of fighting and on four occasions, a police report had been filed by Mercy.
Henry, who spoke to our correspondent, said he did not intend to kill his son but only threw him on the ground.
He said he had caught his father on top of his wife twice and had only released his pent-up emotion on the day of the incident.
However, 36-year-old Mercy, who is at present writhing in pains at Evolution Hospital, Okota, denied having sexual relations with her father-in-law.
She said, "My husband had been quarrelling with his father and had banned me from going to see him but out of respect, I continued to get in contact with my father-in-law.