The third set will be scrapped in doubles matches from next year and replaced with a tie-break.
Santoro and Llodra won the Masters Cup in Shanghai
After trialling the move in recent months, organisers of men's tennis have chosen to go ahead with the change despite some fierce opposition.
The new format will use a first-to-10 tie-break, and no advantage will be played in the first two sets with games decided by the first point after deuce.
"We want to make it more exciting," said ATP chairman Etienne de Villiers.
"We want to get people to watch this wonderful game of doubles."
The decision will not affect Grand Slam tournaments or the Davis Cup, which are run by the International Tennis Federation.
Several of the world's top men's doubles players are to take their grievances over the planned rule changes to court.
The announcement came as Michael Llodra and Fabrice Santoro beat Leander Paes and Nenad Zimonjic 6-7 (6-8) 6-3 7-6 (7-4) to win the Masters Cup.