Bidhya Sagar Das, 33, will appear in court later today over the attack that also left the tot's twin one-year-old sister fighting for life on Saturday.
They were rushed to hospital after a "domestic incident" at their home in Finsbury Park late on Saturday night.
"A baby girl now remains in a critical condition and is receiving specialist medical care", said Detective Chief Inspector Dave Whellams, of the Met's Homicide and Major Crime Command.
He was charged in the early hours of Tuesday and will appear in custody at Thames Magistrates Court later.
The Metropolitan Police's Homicide and Major Crime Command had launched a major manhunt for Sagar and arrested him after 20 hours on Sunday.
The boy, named locally as Gabriel, died from his injuries early on Sunday morning.
The girl, who has been operated on, remains in a critical condition, police said.
"I would still like to hear from anyone who may have any information regarding this awful incident".
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