Hernandez gave up six hits and three walks, while striking out four and keeping the Marlins off the scoreboard long enough for the Mets' bats to do the damage.
Jose Reyes hit a two-run home run and drove in three runs, Luis Castillo ended his 1/10 drought by going 4/4 and Ryan Church continued to rip the ball with two more doubles to take his batting average on the year to .526.
The Mets scored runs in the 3rd, 5th and 6th inning to jump out to a 5-0 lead and they broke it open for good with a three spot in the 8th after the Fish had mounted a slight two-run rally half an inning earlier.
Hernandez, who was 13-11 with a 6.05 ERA with the Twins and Rockies in 2008, was throwing his fastball around 86mph and his slider in the high 70s and the Marlins had no answer for it until they knocked him out of the game in the 7th inning.
Equally important for the Mets was the fact that they went 5/14 with runners in scoring position, in stark contrast to Friday night when they went 1/12 and stranded 14 in the 5-4 loss.
The Marlins had the first chance to strike in the 2nd inning when Dan Uggla and Jeremy Hermida hit back to back singles off of Hernandez to lead off the frame.
But Cody Ross popped up a curveball to centre, Cameron Maybin struck out on a 87mph fastball and pitcher Ricky Nolasco fanned on a two-seam fastball.
With that jam out of the way, the Mets took advantage of the opening they crafted first in the top of the 3rd inning when Jose Reyes got his first extra base hit and RBI on a broken bat line drive double past Jorge Cantu to score Castillo.
Then the gold gloves took centre stage. Hanley Ramirez snagged Daniel Murphy's line drive up the middle to double off Jose Reyes at second base and in the bottom of the inning David Wright returned the favour.
Bonifacio had continued his hot start with a double and he moved to third on Jeff Baker's ground out. Ramirez then smoked a ball towards left field but Wright stuck out his glove hand, snared the ball to get the out and then dove head-first into third base to double off Bonifacio who was frozen a few steps off the base.
Marlins ace Ricky Nolasco, who was 15-8 last year, got into his main period of trouble in the 5th inning and it would be the last inning he would pitch.
Reyes padded the Mets lead to 3-0 by hitting a two-tun home run - his first of the season - on a fastball which caught a little too much of the plate to score Castillo for the second time of the night
Daniel Murphy then singled past the diving Dan Uggla and Carlos Delgado drove him home from first with an RBI double into the right field corner on a hanging slider.
Nolasco's final line was five innings, four runs - all earned - on seven hits and two runs through 87 pitches.
Andrew Miller, who will be the Marlins fifth starter in a few week's time, came in in relief of Nolasco, but the Mets jumped right on him too.
Ryan Church led off the top of the 6th inning with his fifth double in the first five games of the year and Brian Schneider made a productive out to advance him to third.
Castillo then had his third hit of the day to drive him home to give the Mets a comfortable 5-0 cushion.
The Marlins sole runs came on a two-out RBI single in the 7th inning from pinch-hitter Wes Helms and a slap single the other way from hot-hitting Bonifacio.
Brian Stokes gave up the Marlins second run, an inherited run charged to Hernandez, against the only batter he faced, but the Mets broke the encounter open in the 8th inning.
Schneider led off the top of the 8th with an infield base hit and he advanced to second base on Cantu's throwing error after he had knocked the ball down.
Castillo then dropped down a beautiful bunt, intended as a sacrifice, but Bonifacio's throw was slightly off line and Castillo was ruled safe at first as Cantu could not make the play.
Alex Cora drove Schneider home on a ground out to make it 6-2 and Daniel Murphy drew a five-pitch walk to put men on first and second for David Wright who laced an RBI single back up the middle to make it 7-2.
Delgado made it 8-2 with a single of Hayden Penn to right field to score Murphy as Wright went first-to-third, but Beltran struck out to set down the side.
Darren O'Day, who had struggled somewhat in his previous two appearances, retired the Marlins in the 8th and one runner in the 9th, but Cody Ross scored on Ross Gload's sac fly to right to make it 8-3.
Francisco Rodriguez came in to close the game out - a non-save situation - to record the 8-4 win.
He fanned Ronnie Paulino, gave up an RBI single to Ramirez and got Cantu to fly out to end the game.
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