In the All Black side announced this morning to take on the Springboks at Forsyth Barr Stadium, Piri Weepu was named at halfback, and will make his first start of the season in the black jersey on Saturday.
Smith (23) will be on the reserves bench.
All Black coach Steve Hansen said Smith breached a protocol in team recovery last week when the All Blacks defeated Argentina in Wellington.
Hansen refused to say what that breach was and would not be drawn despite questions on the issue.
''Unfortunately for Aaron Smith, we have a strong focus on recovery and he broke a protocol on that area last week so that made him ineligible for selection,'' he said.
"He broke a non-negotiable and the consequences are that you don't start if you break them.''
Though he could not speak for the player, Smith would naturally be disappointed, Hansen said.
Smith had impressed in his six tests so far in what had been a great season for him.
He had started behind Jimmy Cowan at the Highlanders at the start of the season but had rapidly gone past him and his sizzling pass had lead to him making his All Black debut against Ireland in June.
