The wicketkeeper-batsman was also named as Australia's best limited-overs player over the past 12 months, just two days before he heads off to South Africa with the defending world champions for the World Cup.
One-day captain Ricky Ponting was selected as the Test player of the year after making five hundreds in the past 12 months and also finished second to Gilchrist for the major award, decided by votes from players, umpires and media.
Gilchrist joined Matthew Hayden (2002), Steve Waugh (2001) and Glenn McGrath (2000) as winners of Australia's most prestigious cricketing award after a brilliant year with bat and gloves.
Over the past 12 months, Gilchrist has scored 928 runs at an average of 77.33, including three centuries, and 872 one-day runs at an average of 34.88, with two centuries.
Last year's Wisden player of the year, Gilchrist's best performance with the bat was his unbeaten 204 against South Africa in Johannesburg in February, which briefly stood as a world record for the fastest double century in Test cricket.
Less than a week ago, playing against England in Sydney, he equalled his own wicketkeeping world record of six dismissals in an innings of a one-dayer.
"It's been a great year for me but I really didn't expect to win this," Gilchrist told a packed reception in Melbourne.
Queensland batsman Martin Love was named state player of the year while 22-year-old off spinner Nathan Hauritz was chosen as the young player of the year.
Former Test captains Lindsay Hassett and Ian Chappell were inducted into Australian Cricket's Hall of Fame.
