The left-arm quick received 168 votes against Clarke's 156. James Faulkner was third with 121 votes followed by Shane Watson with 119.
Clarke won the Test Player of the Year honour while Aaron Finch picked up the T20 International Player of the Year award.
George Bailey, who was today dropped from the Test squad, was chosen for ODI Player of the Year award.
The award winners
Allan Border Medal - Mitchell Johnson
Belinda Clark Award - Meg Lanning
Test Player of the Year - Michael Clarke
One-Day International Player of the Year - George Bailey
T20 International Player of the Year - Aaron Finch
Domestic Player of the Year - Cameron White (Victoria/Melbourne Stars)
Bradman Young Cricketer of the Year - Jordan Silk (Tasmania/Sydney Sixers)
Australian Cricket Hall of Fame - Belinda Clark, Mark Waugh