Jose Reyes homered twice for the $138 million Mets but committed a two-out error at shortstop in the first that led to two unearned runs.
Pelfrey (2-6) lasted only four innings and dropped his sixth straight start as fourth-place New York (23-26) fell three games below .500 for the first time since Sept. 18, 2005, according to the Elias Sports Bureau.
The Mets have lost seven of eight and 10 of 14 overall. With few fans remaining at Shea Stadium in the late innings, a chant of "Fire Willie!" could clearly be heard.
Earlier in the day, Randolph sat down with owner Fred Wilpon and his son, Jeff, the club's chief operating officer, as well as general manager Omar Minaya to discuss two things in particular: the team's sluggish play, and Randolph's comments last week about his portrayal on Mets broadcasts in which he raised the issue of race.
Randolph subsequently apologized for those statements.
"Willie's job was never in danger going into this meeting," Minaya said. "Willie has my support. He has the support of our ownership. ... There is no limbo period. Willie is the manager."
So, was he told he'll definitely manage the Mets for the rest of the season?
"No, they didn't say that," Randolph answered.
Randolph then met with his players after batting practice, but it didn't help on the field.
Coming off a doubleheader sweep of San Francisco on Sunday, the Marlins made their first trip to Shea Stadium since knocking New York out of playoff contention on the final day of the last season.
Florida looked like the better team on this day, too.
After beating Arizona ace Brandon Webb in his previous outing, Ricky Nolasco (4-3) won his third decision in a row. He allowed three runs and nine hits in five innings.
The Mets stranded seven runners through the first five innings before Doug Waechter, Renyel Pinto and Joe Nelson combined for four perfect innings of relief.
Pelfrey retired his first two batters before Reyes botched Jorge Cantu's one-hop grounder. Ex-Met Mike Jacobs followed with a broken-bat double that scored Cantu, and streaking Dan Uggla added an RBI double.
The Mets came right back in the bottom half with four consecutive hits. Reyes hit his 11th leadoff homer, extending his team record, and New York loaded the bases with none out.
Carlos Delgado hit a shallow sacrifice fly to tie it, but that was all New York got.
Reyes homered to right again in the second for a 3-2 lead before Florida batted around against Pelfrey in the third.
The right-hander loaded the bases with two outs on a single, a walk and a hit by pitch before Gonzalez hit a sinking liner to center that got past a sliding Carlos Beltran for a three-run double. Matt Treanor's RBI single made it 6-3.
Jacque Jones made a jumping grab at the center-field fence in the bottom half to save a run and rob Nick Evans of extra bases.
Delgado, who entered batting .219, was booed after fouling out weakly with two on and none out in the fifth.
Jeremy Hermida added a run-scoring single off Matt Wise in the eighth.
