Halfback Genia polled three votes in the last round of the season to finish on 18, one point ahead of teammate and flanker Higginbotham, Western Force captain David Pocock and Brumbies five-eighth Christian Lealiifano, who missed a significant portion of the season through injury.
Having played every minute of Queensland's Super season and Australia's four June Tests, Genia was happy to be rested from this week's national training camp in Sydney.
"I feel pretty busted up and pretty sore to be honest," Genia said.
"(Wallabies coach) Robbie (Deans) sent me a text after we lost the (semi-final) game to the Sharks and said I could have the week off and I've been really grateful for it.
"Because even lazing around being at home I can feel bumps and bruises and things getting better and healing and I know I will come back into camp next week refreshed."
Queensland coach Ewen McKenzie, who won the coach of the year award, said Genia was competitive and liked to play, so he rested him from training occasionally rather than from matches.
Genia felt all of the other highly placed contenders were probably more deserving of the player of the year title, his second award in an effort only previously achieved by flanker George Smith and fullback Chris Latham.
"For me in particular, Scott Higginbotham can be disappointed to have not received the award," Genia said.
"I really do think he was exceptional for us and I think the biggest thing he has gained in his game is just that consistency week in week out of playing well."
Asked how big a loss Higginbotham would be when he leaves to join Melbourne, Genia said: "A huge loss. He's really established himself as a world class player.
"I really think not just for the Reds but also for the Wallabies in his recent performances."
McKenzie downplayed the imminent loss of Higginbotham.
"When I arrived Berrick Barnes was a massive loss, Daniel Braid was a massive loss and every year we've had massive losses and people say we will never recover from them," McKenzie said.
"But then someone else turns up. They don't just turn up by accident, there are other players out there.
"They might not have exactly the same attributes, but we've been developing a really fine crop of young back rowers, the Ed Quirks, the Jake Schatzs the Liam Gills, these guys have all stepped up."
Queensland also won the awards for team of the year and try of the year for a team effort against the Rebels scored by winger Dom Shipperley.
The improving Brumbies were recognised with their winger and former rugby league player Joseph Tomane named rookie of the year.
Steve Walsh won the referees' award.
