In 2009, Hayes played his 200th AFL game in Round 9 against the Brisbane Lions at Docklands Stadium. During the match he gained 31 possessions in the Saints' 16-point victory. He finished third in the 2009 Brownlow Medal.
Hayes played in 19 of the 22 matches in the 2009 home and away rounds in which St Kilda qualified in first position for the finals series, winning the club’s third minor premiership.
Hayes was recognised for his excellent season with selection in the 2009 All-Australian team as a midfield player. It was his third career selection in the All-Australian team.