The baby awoke grisly, crying and screaming - nothing out of the ordinary - close to midnight and the pair had a "well-rehearsed routine" up until that point, Mr Gibson said.

"He was a normal functioning baby without any injuries. That was all about to change," he said.

"This case is about what happened in those few minutes in the master bedroom."

The man took his son from his partner and said something like, "come here, buddy" before cradling him in his arms while his partner left the bedroom, the prosecutor alleged.

He emerged minutes later with the newborn limp and said, "I think there's something wrong with (him)" before he and his partner performed CPR on the baby, Mr Gibson said.

He said the man later told paramedics the newborn just went limp for no apparent reason, however later scans suggested otherwise.

The baby died in hospital after he sustained catastrophic injuries, with bruises to his scalp, blood on the brain, brain swelling and bleeding to his eyes, Mr Gibson said.

He alleged the man became "momentarily intolerant and frustrated" by the baby's unsettled behaviour before he assaulted him.

“The evidence suggests the nature of the assault was a shaking of (the baby), a striking of (his) head in the form of an application to (his) head - or both,” the prosecutor said.

Mr Gibson stressed the man was not charged with murder, and there was no suggestion he intended to cause his son's death or even seriously injure him.

Defence barrister Rishi Nathwani SC will give his response to the jury on Wednesday.

The trial continues.