Dominating possession for most of the first half, PNG eventually got a result in extra time through scoring machine Meagen Gunemba who fired a shot into the nets after a good cross from Georgina Kaikas.
The downpour did not help both sides especially Cook Islands who could not get past PNG's solid backline.
PNG got their second goal early in the second half after a shot deflected off the gloves of Cook Island's goalkeeper Marjorie Toru and onto PNG'S Fatima Rama who booted it in.
From this point, PNG turned to defence to steer them home to a 2-0 win.
Finals for the women's soccer will start next week.