After a flurry of goals early in the game, with Luke O'Dea scoring twice either side of Glen Trifiro's volley, Heart put the foot down in the second half through Paulo Retre and Alex Dao.
The bottom-placed Mariners did finish the season on a high note with Patrick Dixon scoring a consolation goal deep in second-half stoppage time.
Heart immediately put their stamp on the game in the fourth minute with Dao being brought down in the area by Mariners captain Josh Bingham and O'Dea stepped up to send goalkeeper Justin Pasfield the wrong way from the penalty spot.
But two minutes later the Mariners tied the game through a superb volley touch and volley from Trifiro after quality work from Dillon Vorster down the right flank.
The frantic start to the game continued on 10 minutes as Ersin Kaya played a superb outside-foot through ball to O'Dea, who steadied and calmly slotted the ball in the corner with Pasfield charging out.
O'Dea should have had a hat-trick a few minutes later but could get good contact on his free header in the six-yard box after Kaya's perfectly flighted cross.
Tom Slater was at the forefront of the Mariners' quality attacks in the first half, putting in some quality crosses and having a 25-yard strike superbly saved by Heart goalkeeper Philip Petrovski.
The home side started the second period well with Marcus Schroen and Kaya having shooting directly at Pasfield when they should have done better.
Slater had a golden chance to equalise in the 60th minute but snatched at his shot and put it wide after intercepting a poor pass coming out of the Heart defence.
The Mariners were given a warning sign of what was to come on 68 minutes with Petreski scuffed shot rolling through a mess of bodies in the penalty area to rebound off the base of the post.
Heart eventually got their third goal in the 73rd minute with Retre showing quick feet to bring the ball down and find space before curling a shot in the corner from inside the box.
A minute later, the home side scored again when Pasfield found himself losing the ball near the touchline and after Jeremy Walker's cross was deflected down, Dao managed to toe the ball into an empty net.
Central Coast did pull a back deep in second-half stoppage time after Trifiro's shot was parried into his path and Dixon finished from point-blank range.
Heart ended the season with four wins in a row to finish in fifth place while the Mariners remain in last position.
Melbourne Heart 4 (O'Dea 4'pen 10', Retre 73', Dao 74')
Central Coast Mariners 2 (Trifiro 6', Dixon 90+2')
Melbourne Heart: 2. Jeremy Walker, 3. Philip Petreski (C), 4. Andrew Mullett, 5. David Vrankovic, 6. Alexander Dao, 7. Hernan Espindola (8. Paulo Retre 60'), 9. Luke O'Dea, 10. Marcus Schroen (11. Stipo Andrijasevic 60'), 14. Ersin Kaya (13. Joseph Katebian 60'), 15. Sam Mitchinson, 16. Philip Petrovski (GK) (1. Marco Stevanja 46')
Central Coast Mariners: 1. Justin Pasfield (GK), 3. Joshua Forbes, 4. Adrian Vlastelica, 6. Jesse Curran (2. Lachlan Wales 60'), 7. Dillon Vorster (14. Steve Whyte 60'), 8. Nathan Verity, 10. Dominic Ferguson, 11. Josh Bingham (C), 15. Glen Trifiro, 16. Tom Slater, 17. Dejan Pandurevic (9. Patrick Dixon 55')