Rather than being digested, the magnets gripped together inside him, pinching soft tissue.
His mother, Lila, said her son started feeling ill during a trip to Australia early last month.
"We thought it was because he'd been swimming and he'd swallowed a lot of water and the pool was quite dirty," Mrs Vagana said. "We thought he'd caught a virus."
She took Zeph to a local accident and emergency department where he was given antibiotics and hydrolytes iceblocks.
But not long after they returned home to Avondale in Auckland, Zeph got sick again.
"He had a sore tummy and was vomiting and the stomach cramps were making him walk hunched over - he was in so much pain," Mrs Vagana said.
She took him to the family doctor, and to Starship hospital where he had a chest x-ray and blood and urine samples taken. None gave any insight into what was wrong with him.
"It was quite scary - nobody could work out what was going on ... he kept saying he had this pain right behind his belly button.
"We could see him deteriorating in front of our eyes. He was losing weight and he kept looking more and more sick."
Last Sunday, Zeph walked over to his mother with a small silver ball in his mouth and she "just clicked".
"My daughter had been given a [Buckyballs] set for a present, but I thought they'd been thrown out because my daughters heard a man say on the radio that he swallowed two and they perforated his insides trying to get to each other."
Zeph returned to Starship, and this time a stomach x-ray was taken.
"They called me over and said, 'You'd better look at this' ... You could see a perfect bracelet of these magnets in his bowel."
Zeph had emergency surgery to remove the Buckyballs, which had pierced his bowel as their magnetic fields pulled them together.
Mrs Vagana said she wanted to warn other parents about the dangers of Buckyballs.
The Ministry of Business Innovation and Employment is currently writing advice for Consumer Affairs Minister Simon Bridges.
A spokeswoman for Mr Bridges said he planned to issue an unsafe notice for the product.
More than 200 children around the world, including two Australians, have swallowed the spheres, and many required surgery.
Buckyballs were banned in the United States and Australia this year.
They are made by American company Maxfield & Oberton and sold in New Zealand through websites.
Last Monday, the company said it would stop making them.
