The ARU, whose coffers were only partially replenished by this year's British and Irish Lions tour, have engaged in a raft of cost-cutting measures since new chief executive Bill Pulver took over earlier this year.
The new deal with the Rugby Union Players' Association also includes a $5 million annual salary cap for each of the five Australian Super Rugby franchises.
"This agreement has been achieved through a culture of collaboration and partnership between players and ARU to generate strategies to address the game's current challenges," Pulver said.
"This deal is arguably the most significant of its kind since rugby turned professional in 1995.
"The players have acted with integrity and maturity throughout the negotiations and their support for the game warrants acknowledgement by the Australian rugby community."
The deal, which will run from 2014-17, replaces a previous agreement drawn up almost a decade ago and comes with the ARU facing severe financial challenges.
Although Australia have won the World Cup twice in 1991 and 1999, rugby union ranks third in popularity behind rival football codes Australian rules and rugby league with the professional football league snapping at its heels.
The A$10,000 match fee will go to those "contracted" players whose Super Rugby contracts attract a "top-up" from the ARU, while those without such a deal will get A$12,000 per game.
While the new deal will lead to a pay cut for the top players, the ARU will hand over an increased percentage of "gross player revenue" to the players from the current 26 percent to 29 percent.
"The players have made significant concessions in this deal to ensure that rugby will be a stronger game for those who follow in their footsteps," RUPA chief Greg Harris said.
"The significant contribution the players make to the game has been recognised by formalising an increase in the player's share of revenue and by increasing the minimum salaries paid to players over the period of the agreement."