Cristian Casseres Jr. gave New York a sixth-minute lead before Chris Mueller equalized for the Lions. Fabio settled matters with a 79th-minute strike.
Story of the match
The first real good chance of the match also produced the game's first goal when Orlando City turned it over and the ball eventually cycled to Casseres Jr. on the right and he cut back against an overplaying Lions defense to beat on the far side.
The Lions thought they had pulled even after Mauricio Pereyra won a free-kick at the same time Antonio Carlos went down and he signaled for substitute Rodrigo Schlegel, who wasn't ready. He then stepped up, took the free kick, scored, but was whistled for a foul to wipe out the goal.
Red Bulls goalkeeper Carlos Coronel made a diving save on Mueller in the 16th minute and two minutes later, Michael Halliday fired just wide off of a free kick. Coronel then saved from Pereyra and seconds later, Mueller went just over the bar.
Late in the first half, Orlando City had a prime chance to tie things up as Pereyra drew a foul in the box. The Colombian took the penalty himself, but Coronel guessed right, diving to his left to preserve New York's lead. Daryl Dike had the last chance of the half, heading over from a cross.
The Red Bulls had much of the possession early in the second half and just five minutes in, Antonio Perea turned it over, but the shot went over. In the 53rd minute, Coronel saved from Dike after he had been played in by Junior Urso.
It was a mistake that led to the Lions drawing level. Dike dispossessed Red Bulls defender Sean Nealis and he sent the ball to an onrushing Pereyra, who found Mueller on the left and he beat Coronel under the bar to make it 1-1.
New York nearly took the lead as Patryk Klimala fired inches wide in the 72nd minute and after Coronel saved from Nani, the Red Bulls grabbed the winner.
Orlando City's two centre-back decided to converge on Klimala, but Schlegel left Fabio to Halliday, who was helping Robin Jansson even though he was in good position. Klimala squeezed a pass through to Fabio and he beat Austin to make it 2-1.
Uri Rosell managed a shot deep in stoppage time, but it missed the net completely and New York left Orlando with their second 2-1 victory over the Lions on the season, the only two defeats suffered by the hosts this year.
Man of the match: Patryk Klimala
He led the New York attack in this one, taking five shots and assisting on both goals, the chief architect for all of the Red Bulls success on offense.