But after four hours of deliberations, a jury of six women and six men unanimously found Taylor guilty of murder.
They also found him guilty of assaulting the child the day before the murder.
The Crown had alleged that Taylor was suffering from sleep deprivation, headaches and irritability caused by multiple concussions around the time Ihaka was developing an ear infection, when he "snapped".
Crown prosecutor Mark Zarifeh accepted Taylor had experienced a "momentary loss of temper".
"That, unfortunately, is the case in a lot of these kinds of killings," he said.
Defence counsel Phil Shamy said Taylor maintained his innocence.
The court earlier heard how Taylor told police minutes after the boy's death at the couple's Truman Rd home how he heard two "bangs" in the night and thought he'd fallen in his cot.
Taylor said he lied to police about the fall to protect the heavily pregnant Stokes.
He testified that Ihaka was floppy and breathing raspily earlier in the evening.
Worried that Stokes had done something, he baulked at getting medical help because he didn't want to get her into trouble.
He claimed he would've "gone to prison" for her if she'd admitted hurting Ihaka in a four-hour window when he was out of the house.
But Zarifeh said in his closing address that the medical evidence heard in the trial - which Taylor dismissed, saying "science gets lots of things wrong" - completely undid his story.
UK neuropathologist Professor Colin Smith believed it was a "maximum of minutes" from Ihaka being injured to him becoming unconscious.
Asked to comment on defence suggestions that Stokes inflicted the injuries in the afternoon - at least three hours before Taylor says he found him unresponsive in his cot - Smith replied: "That is not an explanation for the pathology that is present in this case."
Zarifeh said the medical evidence was not consistent with Taylor's account, and also independently showed that Stokes couldn't have inflicted the injuries on the Friday afternoon.
