Niese (6-6) yielded just one walk and struck out five in his second career shutout and first since 2010. The left-hander hurled 78-of-113 pitches for strikes in the gem.
Clinging to a 1-0 lead in the sixth, the Mets used an error by Phillies first baseman Kevin Frandsen to load the bases with one out, and Travis d'Arnaud followed with a sacrifice fly for a two-run lead.
After Philadelphia starter Kyle Kendrick intentionally walked Juan Lagares to re-load the bases, Niese shocked him by bashing a pitch into the left-center field gap, chasing home all three runners as the Mets evened their three-game series.
Kendrick (10-11) allowed five run (one earned) on five hits over six full innings.