The decision gave the Reds a sweep of the three-game series in New York.
Both teams scored twice in the seventh, leaving the score tied 4-4 going into the ninth when Cincinnati's Shin-Soo Choo led off with a double. He advanced to third on an out and the Mets opted to have Bobby Parnell (4-1) intentionally walk Joey Votto.
Phillips bounced a double over first base -- a ball the Mets thought foul -- to break the tie. Todd Frazier added insurance with a two-run double.
Alfredo Simons, who pitched the eighth for Cincinnati improved to 4-1 with the win. Aroldis Chapman allowed a hit and struck out two in earning his 10th save.
The Mets led 1-0 after two batters with back-to-back doubles by Daniel Murphy and Rick Ankiel, who both had three hits. Cincinnati went up 2-1 in the third on a two-run Votto home run only to have New York tie the score on Murphy's sacrifice fly in the fifth.
Phillips and Jay Bruce knocked in runs in the seventh for Cincinnati but Murphy and Ankiel had back-to-back RBI hits, tying the score 4-4, in the bottom of the inning.