Well-taken goals from Nick Fitzgerald and Anthony Caceres in the space of four first-half minutes were enough to secure the result for Phil Moss' side, for whom second place was out of reach after the Western Sydney Wanderers' earlier win over the Melbourne Heart.
The Premier's Plate winners finished their outstanding regular season with a tepid performance in a game in which they failed to find much penetration in the attacking third, with the defeat ending a run of six games without loss.
The visitors conceded the majority of possession to the Roar, but held a solid defensive line and were able to create chances for themselves through quick, precise attacks.
In the first half, Eddy Bosnar launched one of his thunderous free-kicks at Brisbane's goal just before the ten-minute mark, and Michael Theo did well to deflect the effort away from goal with his forearms.
A back-peddling Mariners goalkeeper Liam Reddy almost made a meal of a Matt Smith attempt from over the half-way line, but in the end he got one arm in the way to block the shot.
A fluid Central Coast counter-attack resulted in the game's first goal, as Bernie Ibini played through Storm Roux, who cut back for Fitzgerald to slot the ball home.
Moments later, the Roar came close to equalising when Thomas Broich stormed into the Mariners' area and played a pass back for Besart Berisha, but the Albanian's low shot fizzed wide.
The Mariners then doubled their advantage thanks to Caceres' blistering effort from the edge of the area, which Theo could only watch fly past him into the net.
The influential Ibini then ran from deep and out-sprinted Jade North to give himself an opportunity on goal, but the chance was smothered by the Roar keeper.
The Roar sprung to life just before the interval, with Luke Brattan and Matt McKay combining brilliantly to create a chance for Dimitri Petratos at the back post, but the forward's shot slammed against the upright.
Fitzgerald had the chance to bury the game 50 seconds into the second half, but he failed to make clean contact and blazed a shot over the bar from close range.
Another slaloming Ibini run ended with an incisive pass to Fitzgerald, who was fouled by Ivan Franjic outside the Roar box to set up a free-kick opportunity for the Mariners.
Ibini took responsibility, but his shot was aimed straight at the palms of Theo.
On the hour mark, Broich made space for himself in the area before firing an effort on goal, which Reddy fumbled and Berisha turned in, only to be flagged for offside.
Franjic set up the German moments later, but he skied a difficult attempt from a good position.
Though the Mariners were sitting back more as the game wore on, they were still able to create chances for themselves on the counter, and Fitzgerald was sent through by a Mitchell Duke backheel only to shoot into the side netting.
With ten minutes remaining, big Duke cruised down the right before testing Theo with a low shot.
Berisha then shaved the upright in the dying minutes, but it was too little, too late for the Premiers.
Brisbane Roar 0
Central Coast Mariners 2 (Ftizgerald 24, Caceres 28)
Crowd: 14, 218 @Suncorp Stadium
