Barrett suffered a leg injury in the 26-13 win over Ireland in Chicago last Sunday and will return to New Zealand.
He will miss the test against Scotland at Murrayfield in Edinburgh, kicking off at 4.10am on Sunday (NZ time), as well as the remaining games against England in London on November 16 and Wales in Cardiff on November 23.
Scans confirmed a high ankle injury as well as a minor knee injury.
The 28-year-old will head home on Thursday morning to begin rehabilitation under his Super Rugby Hurricanes medical team.
No replacements have been called into the All Blacks squad.
His brother, captain Scott Barrett, suffered a laceration to a leg which forced in from the field in just the third minute against Ireland and he required a dozen stitches.
He is unavailable for the test against Scotland and it is unclear how long he will be sidelined.
Blues lock Josh Beehre was called in from the All Blacks XV as cover earlier this week.
Fabian Holland and Josh Lord are likely to start at lock against Scotland, with Sam Darry and Samipeni Finau the other options.
Leicester Faninga'anuku replaced Jordie Barrett against Ireland, coming on at centre, with Quinn Tupaea shifting to second five-eighth.
Billy Proctor, Anton Lienert-Brown and Rieko Ioane are all options in the midfield.
The All Blacks team to play Scotland will be named on Thursday night.
