But the Marlins responded against Shaun Marcum (0-2) in the next half inning.
Greg Dobbs singled with one out, went to second on Ruggiano's walk and came across with the tying run on Rob Brantly's single.
Ruggiano took third on the play and scored the game-winner on Green's fly ball to left, handing the Marlins a second consecutive win for the first time this season.
Green also delivered a sacrifice fly in the bottom of the ninth to forge a tie for Miami, which won the marathon opener of a three-game home series.
John Buck homered for the Mets -- his ninth in the month of April.