The left-hander, who has been dealing with tendinitis in his pitching shoulder, will seek to add to his string of solid outings in Sunday's finale of a rain-shortened series.
Although the Marlins own the worst record in the majors, the Mets are just 3-7 in the season series. After getting swept in Florida last weekend, New York fell 2-1 in 20 innings Saturday.
The Mets (23-34) were a team-record 0 for 19 with runners in scoring position in their fifth defeat in six games. Adeiny Hechavarria helped end the longest game in Citi Field history with an RBI single.
The Marlins (17-44) also matched their longest game as a franchise while bouncing back from a three-game sweep in Philadelphia. Miami missed an opportunity to end that skid earlier when Friday's game was washed out due to rains from Tropical Storm Andrea.
"It means a lot. It's huge," Marlins reliever Steve Cishek told the team's website. "We've lost so many close games and so many walk-off games. We really needed something to go our way. This is big for us. It takes a huge weight off us. I'm so glad it went our way."
After having to skip his most recent start, Niese (3-5, 4.40) will try to help the Mets rebound from that marathon defeat. Before developing tendinitis, he posted a 1.33 ERA over three outings but only had a 1-1 record to show for his efforts because of a combined six runs of support from his teammates.
Niese gave up one run over seven innings to the New York Yankees in his most recent start May 27 but did not get a decision in a 2-1 victory.
"He's been bothered with a little discomfort for a couple of starts," manager Terry Collins said. "He was a lot sore after his last start."
In his only start against Miami this season April 6, he allowed two runs over six innings but was not part of the decision in a 7-3 victory.
In this matchup, Niese will pitch opposite New York native Tom Koehler, who is still seeking his first major league victory. Koehler (0-4, 3.70) had allowed three runs or fewer in five major league starts before a 7-2 loss in Philadelphia on Monday.
The right-hander pitched four scoreless innings to start that game but was ultimately charged with five runs over five-plus frames.
"If you execute your pitches, you'll get guys out," Koehler said. "I didn't do that."
Koehler took the loss in his only start against the Mets on Oct. 3, allowing three runs over five innings in a 4-2 defeat. He struck out five in three innings of scoreless relief against them April 29.