The open-topped sports car was created to celebrate the Japanese carmaker's 50th anniversary but, with global sales tanking for most brands, Honda has cut the car to keep its business moving.
Production will end with the last of the 2009 model-year S2000s, which means around the middle of this year.
But Honda Australia is down to just three cars in local stocks and is not expecting to have to re-order.
"It's run its race," says Mark Higgins, spokesman for Honda Australia.
"We've been working on a customer-order basis for the last couple of years. We haven't had too many in stock."
Production of the S2000, which currently lists for $73,590 in Australia, has topped 110,000 cars since the first one was built nine years ago. America topped the S2000 sales charts with 65,000 and Japan was next with 20,000.
"It was introduced in Australia in 1999, which was the biggest year for sales. It did well in 2000 and 2001 but slowed down after that. We have sold 1818," says Higgins.
The S2000 decision comes after Honda confirmed it had canned its planned replacement for the NSX sports car.
It showed a concept at a number of major motor shows but eventually decided it could not justify the spending, or the potentially poor publicity, to put it into full-scale production.
Instead, Honda is looking to hybrids to give it a sporty push for 2010 and beyond. It believes, like Lexus, that a small petrol engine with an electric booster will work best and also give the potential for emission-free electric running in cities.
"We are changing directions and looking more towards hybrids. The CR-Z is slated to be a sports car in the style of the original CR-X," Higgins says.
The production version of the CR-Z is expected at the Tokyo Motor Show in October, although it is unlikely that the two-seater coupe will now be developed into a droptop.
On the S2000 front, Higgins says it's not too late for fans to get a car.
"People can place an order until the end of April. They're looking like collector's items now," he says.