The Marlins third baseman, who has recovered from right wrist surgery, suffered a contusion after being struck on his right hand by a pitch Saturday night.
Murphy was plunked by a 91-mph fastball from Mets lefty Jon Niese in the seventh inning.
Shaking his hand in pain, Murphy was immediately removed from the game.
On Sept. 1, 2010, Murphy dislocated his right wrist, and he underwent surgery the following day.
"It got me on the fat part of the hand, which I guess helped out a lot," Murphy said. "But I honestly feel like the most unlucky guy in baseball right now. That's the way I feel right now. I guess I lucked out on this one."
An X-ray came back negative, and Murphy will be further evaluated on Sunday.
"It will be a day or two," he said. "It's just a little bruise in there. I've got to get it calmed down."
The Marlins wrap up their three-game set with the Mets on Sunday, and they are off on Monday. So Murphy could get two days of rest if he isn't in the lineup in the series finale.
Emilio Bonifacio, Greg Dobbs and Wes Helms are candidates to play third.
Murphy was named the starting third baseman after prospect Matt Dominguez was sent down to the Minor Leagues late in Spring Training.
It's been a rough time for the Marlins at third base. On Friday, Dominguez fractured his left elbow after being hit by a pitch in a Triple-A game. He will be out four-to-six weeks.