Life support for one-year-old Jack Tobin was turned off this morning and a family member confirmed he had since died.
The funeral for Jack and his father Chris Tobin will be held on Tuesday.
NZ Bus chief executive Zane Fulljames said the company was devastated by the sad news that Jack had passed away.
"We are all shattered and devastated by the passing of baby Jack this morning and the death of his father Christopher, and offer our deepest condolences to the family and their loved ones," he said.
"We extend our support to the family and continue to support our driver to ensure their wellbeing following this tragedy. We fully cooperate with the police to assist in their investigation."
Jack's 2-year-old sister Elle is in a stable condition in hospital and expected to make a full recovery after Tuesday's crash.
Their father, 51-year-old Christopher Francis Tobin, died after his car collided with a bus, just minutes from their Mt Eden home.
A Givealittle page has been set up to raise money for his devastated wife Olivia and their children. At the time of writing it had raised nearly $10,000.
Tobin is suspected to have suffered a medical event before the crash on the corner of Mt Eden Rd and Bellevue Rd.
His car crossed a median strip and collided with a double-decker bus.
A Givealittle page set up for the family says Tobin, known as Tuffa, was just minutes away from his Mt Eden home when the crash happened.
"Chris was so full of life, he had one of the biggest grins and a heart full of so much love to all those around him," the page reads.
"He was a devoted family man."
Tobin had three children with Olivia and two older sons from a previous relationship.
"This Givealittle page is one way we can somehow help this beautiful young family get through this terribly tough time and to show them our support.
"Our hearts and prayers go out to you and the kids, Olivia.
Auckland Tramways Union president Gary Froggatt earlier told the Herald he understood the driver of the car had a medical event, swerved across the median strip at some speed and into the oncoming bus.
The police, when asked about the possible cause of the crash and Froggatt's statement, said they were continuing their investigation and couldn't comment until it was completed.
Froggatt said the bus driver, who is married with children and lives in Mangere, had suffered the sort of trauma that would live with him forever.
About half a dozen passengers were on the bus when it crashed. Two suffered minor and moderate injuries and were taken to Auckland Hospital.