Another controversial, tumultuous game saw DC United return to the Eastern Conference final, with the Red Bulls missing a chance to level the game from the penalty spot
In an eventful second half, two red cards were shown, the penalty was missed at the second attempt and the winning goal was scored by United rookie Nick DeLeon.
It gave DC a 2-1 series win on aggregate, following a 1-1 draw at RFK in the first leg.
Both teams saw golden opportunities in the first half go begging.
United's Lionard Pajoy was put through on goal a few minutes in, but Luis Robles was able to get down and smother the chance.
Shortly before the half-hour mark, the Red Bulls could not to capitalize on a chaotic goalmouth scramble, with Kenny Cooper and Thierry Henry having their shots blocked before Joel Lindpere sliced the final effort wide.
The game's crowning drama came close to the 70th minute. Cooper was played through clean on goal, only to have his feet taken out by United goalkeeper Bill Hamid.
Hamid was dismissed, much to the protests of the DC players.
Cooper netted his spot kick past substitute Joe Willis, but referee Mark Geiger called the effort back for encroachment, and Willis kept the second attempt.
That was not the only red card shown on the night. A few minutes later, Rafael Marquez picked up his now-annual playoff dismissal when he was shown a second yellow card for a tough tackle on Chris Pontius.
The visitors finally broke the deadlock in the 88th minute.
DeLeon picked up a smart lay-off from Robbie Russell and beat the offside trap. Showing composure, the rookie finished past Robles to give his side a vital late advantage.
The result means that DC advances to the Eastern Conference final, and will now travel to BBVA Compass stadium on November 11 to take on the Houston Dynamo before returning home to RFK for the second leg.
Australia international Cahill played the full match for New York, his 14th appearance since moving from English Premier League club Everton in July.
He took to Twitter soon after the final whistle: "Hard to take that loss tonight. Massive thank you to the New York RedBulls fans for ur amazing support," Cahill wrote.
He wished DC United all the best before adding how happy he had been with his move to the MLS club: "This last 4 months have been great here at NYRB."
- With Paddy Higgs