The injury saw him miss Queensland's Origin I loss in Brisbane before he made his NRL return for North Queensland in Round 14 before running out on Wednesday to lead the Maroons to victory.
The halfback had scans on an injured shoulder on Thursday with the damage ruling him out for what would've been his 300th NRL match.
He will have to wait until 2018 to tick off the milestone with next season expected to be his last before retiring.
Earlier this year Thurston declared 2017 would be his last in the representative arena so he could dedicate his final year to the Cowboys.
It's not only a huge blow for his club but the Maroons as they head to Suncorp Stadium for the Origin decider on July 12.
The loss of Thurston has been felt by the bookmakers with the TAB pushing the Maroons up to $2.00 (out from $1.75) for game three. The Blues are favourites at $1.80 (in from $2.10).