Griffin was born in Bunbury, Western Australia. His family moved to the southern suburbs of Perth when he was 10 years old, and he attended Booragoon Primary School and Applecross Senior High School, playing junior football for Karoonda JFC. He was drafted by Adelaide from East Fremantle in the West AustralianFootball League with the 21st selection in the 2005 Rookie Draft and spent the 2005 season on the rookie list. He was upgraded to the senior list for the 2006 season but spent most of 2006 playing reserves for Central District Bulldogs. Griffin got his chance to make his AFL debut in the early rounds of 2007 due to the departure of Matthew Clarke and injuries to Rhett Biglands and Ivan Maric. Although he was recruited as a key-forward Griffin was required to play as a ruckman. Many thought Griffin was not yet ready to play at the highest level as a ruckman because of his lanky figure, however Griffin managed to hold his spot for the first 13 rounds of 2007 before being replaced by the returning Maric. Griffin started well in the 2008 AFL season, with strong performances against very good ruck opponents in Will Minson and Ben Hudson, of the Western Bulldogs, Dean Cox and Mark Seaby of the West Coast Eagles and Dean Brogan and Brendon Lade of Port Adelaide. In the 2009 season, Griffin only played 2 games for the Crows, with Maric and Kurt Tippett preferred as the main ruckman with James Sellar and Brad Moran also selected ahead of Griffin. Through his maternal grandfather's Bibbulman ancestry, Griffin is descended from the Noongar people of south-western Australia. He was selected for the Indigenous All-Stars team in 2009. Since returning to his home state of Western Australia, Griffin has been used mainly as Fremantle's backup ruckman, competing with Zac Clarke and Aaron Sandilands for the ruck positions. Griffin played his first game for the Dockers in round 10 of the 2011 AFL season against St Kilda, after Sandilands was unavailable due to injury. A career-best performance against in round 15 saw him collect 26 disposals, 9 marks, 30 hit outs and 2 goals. He played the first seven games of the 2013 season before damaging his anterior cruciate ligament, with the resultant knee reconstruction ruling him out for the rest of the season. He resumed his career in April 2014, through Fremantle's new affiliate team in the WAFL,. Jonathon played in Peel's maiden WAFL premiership in 2016 but missed out in 2017, with a knee injury keeping him out of the Grand Final team. Griffin was delisted by Fremantle at the conclusion of the 2017 season. After being delisted by Fremantle, Jonathon returned to the WAFL in 2018 and was named captain of East Fremantle after having signed a two year deal with the club.
