The news was followed by a statement from Toyota that it was now reviewing its future in the country, raising the possibility of an end to the Australian auto sector.
Holden's decision to move to a national sales company comes after Ford said in May it would stop making vehicles at its unprofitable Australian factories in 2016, with the loss of 1,200 jobs.
With Mitsubishi closing its Adelaide plant five years ago, only Toyota Australia -- which employs more than 4,000 workers -- will be left making cars in the country.
"The decision to end manufacturing in Australia reflects the perfect storm of negative influences the automotive industry faces in the country," GM chief executive Dan Akerson said in a statement.
"This includes the sustained strength of the Australian dollar, high cost of production, small domestic market and arguably the most competitive and fragmented auto market in the world."
Holden, maker of the iconic Commodore car, said 2,900 jobs would be axed over the next four years -- 1,600 from its Elizabeth vehicle manufacturing plant in Adelaide and approximately 1,300 from Holden’s workforce in Melbourne.
It spells the end of a long association with Australia. The company began as a saddlery in 1856 and first started manufacturing cars locally in 1948.
Unions have warned of a multi-billion-dollar hole in the economy and the loss of up to 50,000 automotive industry-related jobs if car manufacturing in Australia ends altogether, and Toyota said it was now examining its options.
"This will place unprecedented pressure on the local supplier network and our ability to build cars in Australia," Toyota Australia said in a statement.
"We will now work with our suppliers, key stakeholders and the government to determine our next steps and whether we can continue operating as the sole vehicle manufacturer in Australia."
The Australian Manufacturing Workers Union said it expected Toyota to follow Holden's lead.
"It's now highly likely that Toyota will leave Australia. In fact it's almost certain," AMWU national vehicles division secretary Dave Smith told reporters.
"It's a very bleak day indeed."
Treasurer Joe Hockey said the government would work closely with the state governments and unions to ensure Holden's departure "does not lead to a significant economic downturn in South Australia or Victoria".
"We will do everything to help in this transition," he told parliament.
Australia's auto industry has struggled against a high dollar for years and Canberra extended a Aus$3.2 billion bailout to the sector at the height of the global financial crisis.
The announcement by Holden follows debate over whether the Tony Abbott-led government should provide more subsidies to the company to keep its doors open or let market forces take their course.
Holden chairman Mike Devereux said the priority over the next four years would be to ensure the best possible transition for workers in South Australia and Victoria.
"This has been a difficult decision given Holden's long and proud history of building vehicles in Australia," he said.
"We are dedicated to working with our teams, unions and the local communities, along with the federal and state governments, to support our people."
South Australia's peak retail automotive business group, the Motor Trade Association of South Australia, lashed out at the government for not doing more to ensure Holden remained in Australia.
"The federal government could have prevented this decision by Holden to close," said chief executive John Chapman.
"Without any certainty of federal support for the industry, the parent company General Motors have weighed up the costs and decided that it's just too expensive to manufacture Holdens in Australia.
"Our attention must now go to those component manufacturers and Toyota, and the federal government must immediately begin working on plans to keep this important manufacturing base in Australia."