Clarke (1167 runs at 68.65 in 11 Tests) and Ponting (837 at 52.31 in 10 matches) polled nine votes but Clarke was awarded the title because he had more three-votes.
Clarke's Test season included five centuries highlighted by his unbeaten 329 in last month's Sydney Test against India.
Mike Hussey was third in the Test award on eight votes alongside Pattinson, whose summer was cut short last month by a foot injury.
Allrounder Shane Watson (553 runs and 11 wickets in 17 matches) beat Clarke (799 runs in 21 games) on a countback to claim the ODI award.
Watson and Clarke polled 19 votes each.
The award went to Watson because he had more three-votes than Clarke.
Watson also pipped Matthew Wade in a two-step countback to win the Twenty20 award.
"It's a great reflection when you look at that leaderboard for the Allan Border Medal, you've got myself, Ricky Ponting, Michael Hussey, Shane Watson, the senior players are on that board and that has played a big part in the success we've had over the last 12 months,'' Clarke said.
Clarke, who had a table of mates from Sydney fly down to support him, paid tribute to his family and friends.
"Any time you mention my family it's quite emotional because I'm so close to them,'' Clarke said.
"I did well not to tear up. We had the indoor sports centre and mum and dad would allow me to train and play there as much as I could.''
Meanwhile Watson said he was stunned with his success.
"It's quite hard to believe. I know a couple of months ago I was struggling physically with my body to even get on the park,'' he said.
"To come tonight and get a couple of awards, it's nice to think I must have performed quite well in the first part of the year because I haven't played much recently.''
Legspin great Shane Warne, who announced his international retirement in 2007, was inducted into the Australian Cricket Hall of Fame.
David Warner, who hit two centuries in his debut Test summer, won the Bradman Young Cricketer of the Year Award.
Victorian opener Rob Quiney polled 52 per cent of players' votes to win the Domestic Player of the Year Award.
Spinner Shelley Nitschke crowned a remarkable career with a fourth consecutive victory in the Belinda Clark Award despite retiring from the international scene in July 2011.
- AAP