While the Reds have endured a injury-ravaged campaign and crashed out of the competition at the first play-off stage, Genia has been one of the shining lights.
He pipped team-mate Scott Higginbotham to the post by a single vote to join former Wallabies George Smith and Chris Latham in winning back-to-back awards.
Former World Cup-winning Wallaby Ewen McKenzie was named coach of the year after steering the Reds to the knockout round.
"While we only had one side in the finals this year there was certainly a great deal shown by a number of the Australian franchises that they will provide big threats in 2013," said Australian Rugby Union chief John O'Neill.
"I want to congratulate the Reds for what they have achieved this season and for securing the awards."
Genia has established himself as one of the finest scrum-halves in the world since making his Wallabies debut in 2009.
The Papua New Guinean-born scrum-half starred during the Wallabies' recent series whitewash of Wales and is likely to be one of the biggest threats to the Lions next year.