The win took the Mets' season win/loss record to 91-58 - a major league-best for the club, and also gave the New Yorkers their first National League East title since 1988.
"This is the biggest stage in baseball," Mets center fielder Carlos Beltran said.
"I'm happy we did it in front of our fans."
The Mets, who had just returned from being swept in a three game series in Pittsburgh, sealed a playoff berth on their home ground in Flushing, Queens in New York.
"It's the greatest feeling in the world," said second baseman Jose Valentin, whose two-run homer in the third innings helped the Mets to victory.
"It's one of the best days in my career."
With 13 games still to play in the regular season, the win over the Marlins put the Mets 16.5 games ahead of Florida and the Pittsburgh Pirates in the National League East, and with cross-town rivals the New York Yankees just three wins away from clinching the American League East title, a possible New York "subway series" is on the cards for the World Series finale.
"This is something you dream about," said Mets third baseman David Wright.
"But it's just the beginning. Our long-term goal is to put a ring on our fingers."
Meanwhile, things weren't looking so good for current World Series champions the Chicago White Sox as they were hammered 8-2 by the Detroit Tigers at US Cellular Field on Monday.
After Magglio Ordonez smashed two home runs against his former team in Chicago, the Tigers lead the American League Central by two wins over the Minnesota Twins with the floundering White Sox a further 3.5 wins behind in third place.
The White Sox close their regular season with a three game series away to Minnesota which could be crucial in the race for the American League playoff wildcard spot.