Flavell returns home after a season with Japanese club Toyota, opting for a switch to Eden Park instead of joining his former team North Harbour.
The 28-year-old forward has played 15 tests for the All Blacks, 43 Super 12 games for the Blues and 59 games for Harbour.
Auckland Rugby Union chief executive officer, David White, said: "Troy is a talented and experienced player who will add value to both Auckland and the Blues in the coming seasons."
White also confirmed the retention of winger Tony Koonwaiyou, who has been rewarded for an impressive NPC season with a one-year contract extension.
"He has grown in stature as a player and we are delighted that he has committed himself to another season with Auckland," White added.
Neither player will be considered for the forthcoming All Black tour of the British Isles, but national coach Graham Henry has confirmed two of the walking wounded from the NPC semi-finals will take part.
North Harbour's influential youngster Luke McAlister and Canterbury prop Greg Somerville will both be considered for the squad, named later this week, despite carrying injuries.
McAlister was taken off early during Harbour's defeat to Auckland, while Somerville suffered a calf injury a week earlier against the same opposition.
On McAlister, Henry told the Dominion Post: "He's pretty sore and he might not have been right to play this week, but it's nothing serious. He's got a sore ankle, a sore knee and a sore thigh."
The former Wales boss confirmed Somerville would also travel, but would not be considered for the opening game against Wales in Cardiff next month.