Drew Stubbs executed a go-ahead squeeze bunt 4, in 13 innings.
Juan Francisco slapped a one-out triple in the right-center field gap off of Dale Thayer (0-3) to set-up Stubbs for the squeeze that went toward third base.
"You do anything you can just to get the bunt down and fair," Stubbs said. "As soon as he went to separate his hands to throw I squared around and just kind of stuck my nose in there to make sure I got it down."
Jay Bruce had three hits, including a two-run homer for the Reds, who have won three straight.
Sam LeCure (2-1) picked up the win with a 1-2-3 12th.
Jose Reyes (.336) continued his pursuit of the first NL batting title in Mets history by going 3-for-6 with a pair of solo home runs. He leads the Brewers' Ryan Braun (.335) ,who went 1-for-2 in Tuesday's game against the Pirates.
"Every time I come up to the plate they make a lot of noise," Reyes said about the support he has been getting from the fans. "They know what's going on and that's good to see. I appreciate that and I just try and do my best."
Bruce gave the Reds a quick 2-0 lead in the first inning with a line-drive home run down the right-field line. The Mets gave Cincinnati another opportunity when they were unable to turn a double play when Joey Votto grounded to second, as Reyes bounced his throw to first.
The Mets cut Cincinnati's advantage in its half in the home first with an RBI single by David Wright.
Reyes tied the game in the third with a solo shot to right-center field, and then gave the Mets a 3-2 lead in the fifth when he circled the bases a second time in as many at-bats.
Votto belted an opposite field home run to left-center field to even the score again in the sixth.
Francisco tied it up in the ninth with a two-out double, which plated Dave Sappelt who came on to pinch run for Devin Mesoraco. Mesoraco slapped a single to left, and reached second when Edgar Renteria singled.
The New York Mets announced on Tuesday that they have exercised the contract option for manager Terry Collins for the 2013 season...Bruce's home run in the first was the 100th of his career...Mets starter Chris Capuano has struck out 45 batters in his past 40 2/3 innings of work...Reds starter Bronson Arroyo's six straight seasons of 200-plus innings was snapped, as he threw 199 innings this season...The Mets fell to 21-28 in one-run games this year.