The prize was for his book Richard Seddon, King of God's Own: The life and times of New Zealand's longest-serving prime minister.
The annual award is made by the Australian Historical Association.
It is given to work, based on original research, judged to be the most distinguished contribution to the history of Australia or New Zealand or to the history of colonisation.
Prof Brooking, a member of Otago University's Centre for Research on Colonial Culture, said winning the prize was also good for the Otago department of history and art history, and the university.
It reflected well on everyone, including librarians and archivists, who had helped him in the 10-year book project, which was ''always going to be a difficult job''.
He had gained support not only from his family and the Otago department, but also from former students and thesis writers and his own teachers, particularly Emeritus Prof W. H. Oliver and the late Angus Ross.
Prof Brooking is the second member of the Otago centre to have won the prize, after Dr Angela Wanhalla won last year with Matters of the Heart: A history of interracial marriage in New Zealand.
Centre director Prof Tony Ballantyne was shortlisted for the prize in 2013 for his book Webs of Empire: Locating New Zealand's colonial past.
Prof Brooking's book is the first major biography of Seddon for almost 60 years.
He hoped the book would help readers ''understand a little better this fascinating man'', and as a ''real person, an important politician'' and not just as a caricature.
Seddon, New Zealand's longest-serving prime minister, was in office from 1893 until his death in 1906.
But he had not always been well understood and was often viewed simplistically as a somewhat autocratic ''King Dick'', or for his jingoistic enthusiasm for fighting in colonial wars, including in South Africa, Prof Brooking said.
Seddon held many Cabinet portfolios and had wide interests, including pursuing a complex involvement with Maori, as well as playing an active role in British imperial affairs, while advancing social legislation.
Having experienced tough conditions on the West Coast, Seddon proved widely influential, including in helping lay some of the key early foundations of the country's welfare state.
These included an old age pension and introducing free-place entry to secondary school education.
He was also influential internationally - putting New Zealand on the map and contributing to the continuing tradition of this country ''punching above its weight'' in international affairs.
Australian historian Prof Alan Atkinson shared the prize with his work The Europeans in Australia, Vol 3: Nation.
