If the Jacks defeat Stirling on June 2, they qualify for the Australia-wide tournament as State Cup grand finalists, with the chance to come up against A-League clubs.
ECU, a lowly 10th on the National Premier Leagues WA table, was not expected to beat Balcatta, which is fourth.
It looked as though Balcatta would be the controlling team at ECU Joondalup Football Stadium, when it scored just seven minutes in.
The Jacks continued to absorb pressure into the second half, before catching Balcatta off guard when Jake Benson-Cooper picked up a loose ball and drove home the equaliser in the 62nd minute. The match was forced into extra time with the scores locked at 1-1.
A keeping error allowed ECU’s Charlie Comyn-Platt to give the home side the lead just two minutes into extra time.
Then the Jacks’ Tommy Amphlett iced the game with an impressive volley from the edge of the box in the 116th minute.
NPL WA action resumes on Saturday.