As Fishfins reported in the comments, justice prevailed and the Marlins win stands.
Major League Baseball on Tuesday afternoon denied a protest filed officially on Monday by the Yankees, allowing Sunday's result to stand.
Working in favor of the Marlins was Rule 3.05, which states:
"If an improper substitution is made for the pitcher, the umpire shall direct the proper pitcher to return to the game until the provisions of this rule are fulfilled. If the improper pitcher is permitted to pitch, any play that results is legal. The improper pitcher becomes the proper pitcher as soon as he makes his first pitch to the batter, or as soon as any runner is put out."
Additionally, Rule 3.05(c) Comment reads: "If a manager attempts to remove a pitcher in violation of Rule 3.05 (c) the umpire shall notify the manager of the offending club that it cannot be done. If, by chance, the umpire-in-chief has, through oversight, announced the incoming improper pitcher, he should still correct the situation before the improper pitcher pitches. Once the improper pitcher delivers a pitch he becomes the proper pitcher."
The protest was just the despartion of lost soles, or however the saying goes. There was never any chance of it being upheld. Be that as it may, the Fish finally get to put it in the win column and that is a good thing.