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Emergency services were called to the building on Belmont Rd in Paeroa just after 9pm to find it burning fiercely.
The shop is now called the Pizza Box, but used to be Mykonos Pizza, which was owned by Mr Voudouris.
The 55-year-old was gunned down outside the store in 2012.
The case remains unsolved.
Viv Leonard, who was a good friend of Mr Voudouris, owns the antiques store next door, which also came close to succumbing to the flames.
"We had our first show in 45 years in Paeroa's old picture theatre, and it was a show from Liverpool so it was a really big deal for Paeroa," she said.
"In the middle of it the fire sirens started going and people were thinking it must be a car accident. But then a message got through that the shop next door to mine was on fire."
Her shop, Arkwrights Antiques, was full of smoke while flames were pouring out of the pizza shop.
"There were flames shooting through the roof when the fire brigade got here. And this shop's over 100 years old so it would have just gone up," she said.
"It was pretty scary there for an hour or so until they got the flames under control. They just did so well to get it under control."
A garden memorial that Ms Leonard made to Mr Voudouris at the back of the shop wasn't damaged.
"Jordan was my neighbour for eight years and he was always really lovely and helpful and he was a great guy. So yeah, that was pretty sad," she said.
"And then for this to happen, it was like, 'Oh my God'. So I'm starting to think the place is a bit doomed actually."
The pizza shop had been sold two or three times since Mr Voudouris' death, she said.
Mr Voudouris was found lying in a pool of blood at the rear of his shop early on 18 June, 2012. A $50,000 reward for information has not been claimed.
The death of the much-loved pizza shop owner left his family and the small Paeroa community completely stunned and desperate for answers.