Garrett Jones went 2-for-4 with a two-run shot and three RBI while Josh Harrison knocked in a pair of runs on two hits for the Pirates, who evened their four-game series at one win apiece.
Wandy Rodriguez (12-13) went six complete innings to earn the victory, allowing three runs on four hits. He walked two and struck out three.
Mets starter Collin McHugh (0-3) was rocked for seven runs on five hits before exiting after just 1 1/3 innings.
David Wright launched a solo homer and added a two-run single for New York.