Greenstone Energy, which is jointly owned by the New Zealand Superannuation Fund and Infratil, announced it would not reopen the service station, the company's first closure since buying 220 Shell retail service stations in April.
The Otago Daily Times understands the site was earmarked for closure later this year - the accident accelerated the process.
"We can't afford to run a business that is unprofitable," Greenstone retail general manager Mark Forsyth said.
Last Thursday, a driver of a Ngai Tahu Seafood truck misjudged his entry into the forecourt, resulting in extensive damage to the canopy and building.
After the accident, the company announced it would review the future of the Waikouaiti station.
Mr Forsyth said the site was economically unsustainable, with low and declining sales, and "faced with the rebuild of an already loss-making site, we have had to take the decision to close Waikouaiti".
The company had decided to concentrate on the nearby Palmerston site, on which it recently spent $215,000 upgrading the shop and installing new pumps as it had "a decent chance of economic survival in the long term".
The company would offer employment at its service stations in Palmerston and Dunedin to the six staff affected by the closure.
Greenstone Energy had contacted community members and Dunedin Mayor Peter Chin, who wrote a letter to the company about their plan to close the site, to inform them of the latest development.
Mayor Chin said while he could understand the company's reason for closing the site, it would be disappointing for the Waikouaiti community, which was used to having their own service station.
