Danny McBreen's 42nd minute strike at Gosford's Bluetongue Stadium earned the Mariners their fourth final appearance. They will meet debutants Western Sydney Wanderers in Sydney next Sunday.
After the initial sparring, Mile Sterjovski's 14th minute long-rang effort was the first decisive strike which Melbourne goalkeeper Nathan Coe foiled.
A barren first half was looming when Bernie Ibini received the ball inside the Melbourne half, slipped past a couple of defenders before setting up McBreen and the veteran striker hammered it low and hard from outside the box.
Melbourne nearly equalised at the hour mark but Mariners goalkeeper Mathew Ryan denied Archie Thompson who kicked it straight to him to squander his team's first shot at the Mariners' goal.
Mitchell Duke could have doubled Mariners' lead but his powerful 70th minute strike went wide.
For the Mariners, the only sour note was Nick Montgomery picking up his second yellow card after a late foul on Mark Milligan which will cost the combative midfielder a final appearance.