DC came close to breaking the deadlock in spectacular fashion early on when Nick Deleon cut inside from the left wing to target the bottom corner, but Luis Robles reacted impressively to keep his powerful strike out.
New York looked the most likely to break the deadlock for much of the first half, despite the best opportunity falling to the visitors when Bobby Boswell headed Fabian Espindola's cross wide at the back post.
The momentum soon changed when DC were reduced to 10 men before the break as a shocked Espindola was shown the red card just moments after catching Dax McCarty.
It was no surprise to see the Red Bulls take control of the match in the second half, with Thierry Henry twice going close as one effort drifted wide before a second shot was tipped past the post by Bill Hamid.
Chances continued to arrive for Henry, who proved that it wasn't to be his night when he headed a Saer Sene cross inches wide of the target.
The deciding goal finally arrived in the first minute of stoppage time when Henry found space in a congested area before crossing for Sam, who tapped in from close range to secure victory for New York.