The Rev Canon Dennis Urquhart, who carried out the half-hour church service, said Pene was being comforted by Mr Matthews and other family members throughout.
She got up at the end in front of the crowd of about 200 people to thank them for coming.
"It was very emotional, lots of tears, especially when we closed the lid on the casket."
The boy was found dead by paramedics on Friday morning. Results of an autopsy were inconclusive and it may be up to six weeks before police know whether the baby's death was caused by child abuse.
Detective Senior Sergeant Mark Loper said yesterday it was too early to say whether the investigation would be upgraded to a homicide.
"We will await the final results of the [autopsy]. It could be up to six weeks away [to decide] whether or not there will be any charges in relation to the death at all."
Child, Youth and Family general manager operations Lorraine Williams said the other children at the house were still in the care of their father and other family members.
It emerged yesterday that the toddler had been taken from his mother soon after birth and placed in the care of his uncle by CYF.
Barrister Kathy Jackson represented the baby in the Family Court, and told the Rotorua Daily Post she was devastated to hear the news the baby had died.
St John district operations manager Norm Riedinger said yesterday that the baby was dead in the lounge when the ambulance arrived.
He was unable to comment on the baby's injuries while the case was being investigated.
"Times like these are very upsetting for us, when a young person has died. It affects people no matter who you are."
