Yang was sentenced to death on Monday with a two-year suspended execution, and had all of his property confiscated, the Chinese foreign ministry said.
The Beijing court found him guilty of "espionage", a ministry spokesman said.
The sentence sent a chill through Australia-China relations, which had been improving after a years-long standoff.
Australia has conveyed "our dismay, our despair, our frustration, but to put it really simply, our outrage at this verdict", Prime Minister Anthony Albanese told reporters in Canberra.
"This is a very harsh sentence on Dr. Yang, who is a man who's not in good health, and we will continue to make the strongest representations," the Australian leader said.
Australia's foreign ministry said it understood the sentence may be commuted to life imprisonment if no "serious crimes" are committed for two years.
The Chinese-born Australian citizen has been in jail since 2019 on spying allegations.
The writer, whose pen name is Yang Hengjun, has denied the allegations, telling supporters he was tortured at a secret detention site and that he feared forced confessions may be used against him.
Beijing on Tuesday rebuffed Canberra, insisting that "Chinese judicial organs handle cases in accordance with the law".
"We urge the Australian side to truly respect China's judicial sovereignty," foreign ministry spokesperson Wang Wenbin said.
- 'We must disagree' -
Albanese said his government had summoned the Chinese ambassador to Australia, Xiao Qian, on Monday and would make representations "at all levels".
"We have said very clearly that we will cooperate with China where we can, but we'll disagree where we must. We must disagree with this harsh action by China. We have done so. We will continue to do so," Albanese said.
The prime minister declined to say whether he would withdraw his invitation last year for Chinese Premier Li Qiang to visit Australia.
"We'll respond directly and clearly and unequivocally to China. What we won't do is conduct diplomatic negotiations through the media," Albanese said.
Richard McGregor, East Asia analyst at the Sydney-based Lowy Institute think tank, said the sentence should be seen in the context of China's Ministry of State Security taking a "much higher profile" in the past year, including with social media posts under its own name.
Australia's prime minister had managed to put a floor under relations with China in the past 18 months, McGregor said.
"This is a reminder that there is also a ceiling."
Tensions between Canberra and Beijing mounted in 2018 when Australia excluded the Chinese telecommunications giant Huawei from its 5G network.
- 'Harrowing news' -
Then in 2020, Australia called for an international investigation into the origins of Covid-19 -- an action China saw as politically motivated.
In response, Beijing slapped high tariffs on key Australian exports, including barley, beef and wine, while halting its coal imports.
Most of those tariffs have been lifted under the centre-left government of Albanese, who made a breakthrough trip to Beijing in November 2023, hailing progress as "unquestionably very positive".
A thaw in ties seemed to be confirmed when Australian journalist Cheng Lei was released in October last year after more than three years' detention on espionage charges widely seen as politically motivated.
The severity of Yang's sentence appeared to catch the Australian government by surprise, with Foreign Minister Penny Wong describing it Monday as "harrowing news".
Yang's friends said last year that he feared he would die in jail without proper medical treatment because of a cyst growing on his kidney.
"If something happens to me, who can speak for me?" the writer said in a note shared with friends and supporters.
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