It was the first shutout for Batista (5-2) since 2006 and fifth of his 17-season career. He walked two and struck out five.
Batista allowed a first-inning single to Edgar Renteria and a double to Chris Heisey leading off the second. He retired the next 11 batters, a string that ended with his first walk. He finished the game by getting the last 10 Reds he faced out.
All three Mets' runs were allowed by Cincinnati starter Edinson Volquez (5-7), who gave up six hits in seven innings while walking one and striking out five.
Nick Evans singled in Willis Harris, who reached as the lone Volquez walk, in the fourth inning and Mike Baxter hit a two-run home run in the sixth. It was his first major-league home run.
New York ends the season with a 77-85 record, which is fourth in the National League East. The Reds wound up 79-83, third in the NL Central.