The answer to this can be found late in Chapter 15. It can be found on pages 319 and 320 in the paperback edition of the book. As with everything else in this book, the answer has to do with geography.
In this chapter, Diamond contrasts New Guinea with Australia. He says that New Guinea was not suited for European colonization. Australia, on the other hand, was very suitable. Diamond points out that some of Australia is made up of zones with temperate climates. These areas are good for growing wheat, barley, apples, grapes, and other plants domesticated in other temperate areas. Some areas of Australia are tropical and are good for growing species like bananas and citrus that were imported from other tropical areas. Sheep could thrive in the desert areas of Australia and cattle in the wetter areas.
So, the problem for Aborigines was that their land was really well-suited for growing crops once those crops were brought to Australia. The crops had not been there before, so the Aborigines could not use them. But when the crops were brought, Australia was a great place for Europeans to live and conduct agriculture. Therefore, they conquered Australia even though they could not conquer New Guinea.