Frenchwoman Sandra Matute gave the Freedom the lead on a free kick from 24 yards in th 14th minute.
Kendal Billingsley, whose foul led to Matute's free kick, evened the score in the 37th minute when she connected on a header to put away Mexican Iris Mora's corner kick.
In the 86th minute, Mora was on the receiving end of Kirsty Yallap's cross and scored when she chested the ball down, turned and fired past Freedom keeper Eliza Bennett-Hatton from 14 yards for the winner.
The Blues the third club in W-League history to claim back-to-back championships after the Raleigh Wings (1998-99) and Boston Renegades (2001-02).
"It feels so good to have two undefeated seasons, and I am so happy for our girls," said Pali coach Charlie Naimo, who also serves as WPS's Los Angeles Sol general manager. "It's such a fantastic feeling, and you couldn't ask for anymore effort than what has been given by this team all year."