Emeritus Professor Horner shared the Prime Minister's Prize for Australian history with Ross Coulthart for his book Charles Bean.
It's the second major award for the book and Professor Horner, who is an Official Historian of Australian Defence History at the Coral Bell School of Asia Pacific Affairs at the ANU College of Asia and the Pacific.
In April, he won the UK's Intelligence Book of the Year award in London.
The first volume, released in late 2014, sheds new light on a conspiracy theory that ASIO and the government engineered the Petrov defection, specifically to embarrass the Labor Party and keep it out of power.
The book also outlines tactics ASIO used in counterespionage, from embassy bugging to surveillance of local suspects.
"Throughout his fascinating narrative, Horner details many activities of our nation's spy catchers that have never been published," the Prime Minister's Literary Prize judges said.
Professor Horner's recount of the people who staffed ASIO was that they were 'normal, honourable, everyday Australians', the judges said.
"But as the book demonstrates, those men and women who worked, often obsessionally, to protect our national (and sometimes international) security, were far from being 'normal' or 'everyday'."
Professor Horner said he was delighted with the latest public recognition for his book.
"I am extremely pleased that official histories are being recognised as making a major contribution to Australian history," he said.