The 23-year-old New South Wales right-hander polled 54 votes from team-mates, media and umpires to beat fellow batsman Damien Martyn (51). Vice-captain Adam Gilchrist was third on 41 votes.
Clarke is the youngest winner of the award.
His victory was only the second occasion, after Steve Waugh won in 2001, when the medallist did not win either of the Test or one-day player awards.
Martyn, who scored six centuries in 2004, won the Test award, while Clarke was pipped by Andrew Symonds for the one-day award.
Clarke scored 151 on his Test debut against India in Bangalore in October and claimed 6-9 with his left-arm spinners in the same series in India. He then produced 141 in his first Test in Australia against New Zealand in Brisbane in November.
Clarke, who also scored two limited-overs centuries as an opener, edged past Martyn in the final match of the voting period when he earned a maximum six votes for his 75 not out in Australia's loss to Pakistan in Perth.
Queensland's Andy Bichel won the state player title and South Australian Mark Cosgrove won the Bradman Young Cricketer trophy.
Rod Marsh and the late Clem Hill, a batsman in 49 Tests from 1896-1912, were inducted into the Australian Cricket Hall of Fame.
The Australian voting period counted Test and one-day performances from Australia's tours to Sri Lanka, Zimbabwe, Europe and India last year, last (southern) winter's home series against Sri Lanka, and the home (southern) summer against New Zealand, Pakistan and the West Indies.