Heading into their home clash with the fourth-placed Union, the Red Bulls had just four points from six matches.
But goals from Thierry Henry and Lloyd Sam at Red Bull Arena fired New York level on seven points with Union, who are winless in five.
The Red Bulls - winners of the Supporters' Shield in 2013 - held on for all three points, despite a red card to defender Ibrahim Sekagya with 12 minutes to play.
Henry fired New York ahead on 57 minutes, converting from a cut-back from Roy Miller.
Eric Alexander was the provider of New York's second, whipping in a cross from the left to find Sam, who nodded home to double the hosts' lead.
Union would receive a lifeline back into the contest when Ugandan defender Sekagya threw an arm at a goal-bound effort to hand the visitors a penalty, and also the numerical advantage.
Sebastien Le Toux tucked away the spot-kick, however Philadelphia could not produce another.
