The 31-year-old run machine polled 22 votes at Monday night's Allan Border Medal function, well clear of Mike Hussey, on 15, with Hussey's runner-up finish highlighting the void left by his recent test retirement.
Wicketkeeper Matthew Wade was in third spot, on 12 votes, ahead of left-arm quick Mitchell Johnson (11).
The voting period included nine tests - the three-test series in the West Indies in April and home series against South Africa and Sri Lanka this summer.
Clarke scored 1080 runs at an average of 77.14 over that period, including magnificent back-to-back double-centuries against the Proteas and another ton against Sri Lanka.
He was 334 runs clear of Australia's next top scorer, Hussey.
Clarke's tally of 1595 in 2012 was the fourth-highest by any player in a calendar year, although the start of that period did not contribute to Monday night's award.
He put his stellar year down to hard work and the strong support of teammates.
"Hard work, dedication and some great team support has certainly played a big part, not only in my own performance but in regard to taking over the captaincy," Clarke said.
He said team-wise, it had been an improved year in test cricket but in the one-day format Australia remained too inconsistent.
Last February, Clarke was named both test player of the year and won the Allan Border Medal, which takes in all three formats.
