Orlando's major new signing Kaka came close not long after when he sent a rasping shot just a few inches wide of the New York goal, with Josh Saunders looking stranded.
The Brazilian was not far off again just before the break when he controlled and rifled an effort at goal, which Saunders managed to beat away with a strong palm.
David Villa was a little subdued for City, but he came to life with just over 20 minutes remaining when he slipped a delightful through-ball into the path of Khiry Shelton, who dragged his shot across the face of goal.
The away side had offered very little going forward in Florida, yet they took the lead in the 76th minute through Mix Diskerud, as he collected from Villa to curl past Donovan Ricketts and secure the franchise's first ever MLS goal.
Orlando fans were furious 10 minutes from time when Cristian Higuita was brought down in the New York box, only to be booked for simulation despite strong appeals for a penalty.
Hopes of an Orlando equaliser took a blow in the closing minutes of the game when Aurelien Collin was shown a straight red card for a high challenge.
However, Kaka had other ideas as his free kick took a deflection in the dying embers of the game to wrong-foot Saunders and earn the hosts a last-gasp draw against the odds.