The Lancashire all-rounder has been struggling to gain full fitness after a hernia operation and his place has gone to Yorkshire's Craig White.
The news that Flintoff is not ready for the match comes as a great disappointment to England and is sure to draw some criticism for the team management.
Flintoff played in this summer's series against India despite needing an operation, with the team management suggesting that there would still be plenty of time to recover.
Stiffness
But although he was fit enough to bowel 18 overs in a warm-up match with Queensland, he suffered stiffness and was deemed to be unready for the rigours of a match with the world champions.
Confirming the decision, coach Duncan Fletcher said: "We had a tough choice to make in the all-rounder position between Andrew Flintoff and Craig White," Fletcher admitted.
"But we just felt that the first Test has come round a couple of days too early for Andrew following his comeback from a hernia operation.
"We had concerns about how his body would react to the demands of a five-day game."
Late call-up
England could now arrange a low key match for Flintoff to help him back to full match fitness.
His replacement White was not included in the initial touring party, but got the call when it became apparent that Flintoff was struggling.
White is one of four seamers in the team, along with Matthew Hoggard, Andrew Caddick and Simon Jones, while Ashley Giles and Michael Vaughan are the spin options.
The batting line-up virtually picked itself, though former Lancs captain John Crawley is lucky to get in ahead of Robert Key. The Kent man has been far more successful so far on the tour and is seen as a good long-term prospect for his country.
The only surprise in the Australian selection is their choice of Andy Bichel over the erratic Brett Lee.
Teams:
Australia: Steve Waugh (captain); Adam Gilchrist (Wk); Matthew Hayden; Justin Langer; Ricky Ponting; Damien Martyn; Darren Lehmann; Shane Warne; Jason Gillespie; Andy Bichel; Glenn McGrath
England: Nasser Hussain (captain); Alec Stewart (Wk); Michael Vaughan; Marcus Trescothick; Mark Butcher; John Crawley; Craig White; Ashley Giles; Simon Jones; Andrew Caddick; Matthew Hoggard
Should Freddie have been picked? Have your say.
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