Dunstan St neighbours heard what they described as a powerful earthquake, while others said there had been a "twister" in the street.
A MetService meteorologist called it a "rogue gust".
Kerry McAuley, owner of the affected property, said she was just grateful no-one was hurt.
About 3pm, she got a phone call at work informing her the wind had "peeled back" the roof of her house.
When Mrs McAuley arrived home she saw the back half of the roof of her house had "gone" and rang the fire brigade.
She soon heard the damage had started at the far end of the street, on the other side of nearby Seaton Square.
The wind then hit the neighbour’s house on the other side of the street.
"It took the roof off our place and hit the boys’ [house] next door and shifted their garage," she said.
"I was just grateful that nobody was hurt.
Houses can be repaired and furniture can be replaced."
Neighbour Joel Gavan was home with his partner and a friend at the time.
At first he thought it was an earthquake.
"You know the noise of an earthquake? Times it by 10," he said.
"We just saw swirling out the front and tons of banging and stuff."
His garage was shunted into his house, the trusses in the middle started bowing, some cracked.
A Fire and Emergency New Zealand spokesman said two crews from Clyde and Alexandra responded about 3.20pm. Staff remained on site until 5pm.
A police spokeswoman said there was "quite a bit of property damage" in the area.
A spokeswoman from Aurora Energy said fault response staff had to remove some debris from a power pole and power was briefly cut so they could do that.
MetService meteorologist David Miller said the wind gust was likely a "mountain wave", when wind rushes down the side of a mountain.
While there were wind warnings for eastern parts of Otago, no warnings were in place for the Clyde area — but the wind yesterday had been highly variable.
The "rogue gust" would have been very localised and difficult for the MetService network to pick up.
It was not, as some had suggested, a tornado. Those were associated with thunderstorms, he said.
