The 35-year-old spent almost two months in Tokyo's Tsukuba Memorial Hospital, where he was admitted on December 19th after inexplicably finding it difficult to walk.
The mystery illness was later diagnosed as lumbar discitis.
Thomson, who played 29 Tests for the All Blacks, expressed relief at his release in a social media post.
"57 days in hospital. 1 week of parole. Doctor just clears you to fly home.. Feels good man!," he said on Instagram.
"Thank you to everyone that supported me on this road to recovery."
Thomson made his Super Rugby debut for the Highlanders in 2006. He wasn't selected by the Otago province the following season but returned to the side between 2008 and 2012, the same years he won his New Zealand caps.
He played for the Reds in 2015 and the Rebels the following year.
He had also been playing for the Canon Eagles in Japan since 2013.