The scores were tied at the final siren, with the Saints emerging one-point winners 7.10 (52) to 7.9 (51) in extra time in Lancelin.
The Pirates, who won the flag last year, were favourites to claim back-to-back premierships after finishing the season on top of the table.
Dandaragan will face Cervantes, featuring former West Perth league players Brent LeCras, Dan Hunt, Callum Chambers, Josh Pearce, Clayton Lasscock and Tyson Lord, in the grand final in Moora this weekend.
Cervantes, who finished second, defeated the Pirates 16.10 (106) to 10.11 (71) in the second semi final in Lancelin earlier this month. About 500 people turned out for the clash between the two best sides in the competition, including West Coast sharp shooter Mark LeCras who was there to support his brother and former club.
The older LeCras was named runner-up best and fairest in the league�s JJ Lisick Medal count, with Pirates player Aaron Jarvis winning.
The Cervantes reserves are also through to the grand final.