Gregan added to his successes in 2001 and 2004, polling 50 votes from his peers to beat Waratahs hooker Adam Freier (40 votes) to the award, while Reds flanker David Croft and Brumbies centre Stirling Mortlock shared third with 29 votes.
Gregan, who holds the world record for the number of Tests (127), has endured considerable speculation about his international future, and missed the recent tour of Europe.
But it is apparent he still holds great esteem among the 132 members of the Rugby Union Players Association, who voted him Australia's best when it came to excellence both on and off the field in the areas of performance, leadership, consistency and discipline.
All the members of the squads for the four Super 14 teams, the Brumbies, the Western Force, the Waratahs and the Reds, voted on the award.
Queensland fly-half Berrick Barnes was also honoured, named the winner of the inaugural RUPA best newcomer of the year award.
Barnes was judged most deserving out of all first year contracted players and was awarded the prize ahead of Brumbies pair and brothers Anthony and Saia Faingaa.