Luckenbill had failed to hold on to Kandace Wilson's cross, leading to the Blues' second goal in five minutes. In the 83rd minute, Pali equalized when defender Amy LePeilbet sent Rosie Tantillo's corner kick past Luckenbill.
Indiana had threatened in the first half, but it was held scoreless until the 47th minute when Jessica O'Rourke scored on a header off Mexican international Fatima Leyva's curling corner.
With the win, the expansion Blues finished their season with a perfect 14-0-0 record. LePeilbet was named the Most Valuable Player of the W-League Championship.
FC Indiana Lionesses 1 Seattle Sounders 0
IND: Fatima Leyva (Laura Del Rio) 87
Pali Blues 2 Washington Freedom 0
PAL: Danesha Adams (Collette McCallum) 26
PAL: Danesha Adams 82
Washington Freedom 2 Seattle Sounders 0
WAS: Christie Welsh (Ella Masar) 11
WAS: Ali Andrzejewski (Sarah Huffman) 86
Pali Blues 2 FC Indiana Lionesses 1
IND: Jessica O'Rourke (Fatima Leyva) 47
PAL: Amy LePeilbet (Rosie Tantillo) 83
PAL: Ilaria Pasqui (Kandace Wilson) 88