Javier Vazquez tossed six scoreless innings 1 victory over the Pirates to finish off a season sweep of Pittsburgh.
Florida won all six of the meetings between the teams this year and 12 of the last 13 games overall.
Vazquez (10-11) scattered three hits and two walks while fanning seven.
"I hope we can get [Vazquez] to 12-11," said Marlins manager Jack McKeon. "He's a classy kid, he never complains, he's always ready and he does whatever you want him to do."
Leo Nunez faced the minimum in the ninth to earn his 34th save of the year.
James McDonald (9-8) allowed four runs on five hits and four walks through 4 2/3 innings to take the loss for the Pirates.
Jason Jaramillo brought in the lone run for Pittsburgh, losers in five of its last seven games.
Florida left runners in scoring position in two of the first four innings, but was able to break through in the fifth. Vazquez led off the frame with a walk, and after Emilio Bonifacio lined out to short and Omar Infante flew out to center, scored when Greg Dobbs pulled a double into right field.
Gaby Sanchez then singled in Dobbs, and Murphy followed a Bryan Petersen walk with a two-run double off the base of the wall in right-center field to knock McDonald out of the game and give the Marlins a 4-0 lead.
"There's been some games where it's gotten away from James for an inning, and I think that was kind of the case today," Pirates manager Clint Hurdle said about the fifth inning.
Pittsburgh got on the board in the seventh inning against reliever Clay Hensley. Josh Harrison singled with one out, advanced to second on a groundout by Ronny Cedeno and came home on Jaramillo's single to center field.
The Pirates had a chance to take control of the game when they loaded the bases in the second inning. Ryan Doumit worked a one-out walk and Ryan Ludwick followed with a single. Harrison then grounded into a fielder's choice to put runners on the corners.
After Harrison stole second, Cedeno walked to load the bases. But McDonald went down swinging to end the threat.
Pittsburgh signed general manager Neal Huntington to a three-year contract extension Sunday...Vazquez has won his last three starts. He is now 7-3 in 16 career starts against the Pirates...Pittsburgh has lost seven of the last nine games McDonald started.