The 40-year-old Batista (5-2) walked two and struck out five for the Mets, who snapped a three-game losing streak and finished 2011 with a 77-85 record.
"I do think there is a lot of reason for optimism," said New York third baseman David Wright.
Edinson Volquez (5-7) gave up three runs on six hits over seven innings for Cincinnati, which posted a 79-83 mark one year after capturing the NL Central title.
"[Volquez] threw the ball well enough to win," said Reds manager Dusty Baker.
Looking to become the first batting champion in Mets history, Jose Reyes was taken out after a bunt single in the first. The hit raised Reyes' average to .337. His closest competition, Milwaukee's Ryan Braun, went 0-for-4 Wednesday night and wound up with a .332 average.
Nick Evans put New York on the board with an RBI single in the fourth. Mike Baxter extended the lead with his first major league home run, a two-out, two- run blast to right-center in the sixth.
The Reds were vying for their first three-game sweep in Flushing since April 13-15, 2001...Batista recorded his 11th career complete game...Edgar Renteria and Chris Heisey notched the hits for Cincinnati.