Ten man United came from behind to triumph in extra-time for a record-equalling 12th FA Cup success over Alan Pardew's Palace at Wembley.
Undeservedly trailing through Jason Puncheon's opener, the Reds mustered a performance of resilience and character to level through Juan Mata before Jesse Lingard's stunner ensured a first trophy in the post Sir Alex era despite Chris Smalling's red card.
Connor Wickham thought he had scored on 19 minutes when he rounded David de Gea and slotted in, only for Mark Clattenburg to bring play back for a foul.
A superb challenge by Rooney thwarted former Red Wilf Zaha before the captain curled inches wide from distance at the other end.
Wayne Hennessey saved well from Mata, Marcus Rashford shot wide and Marouane Fellaini went close with a deflected header before Joel Ward brilliantly cleared off the line from Anthony Martial late in the half.
United were left to rue their luck when the woodwork was rattled twice in quick succession shortly after the break, first through Fellaini's powerful effort and then Martial's header.
Marcos Rojo and Rashford were then both forced off through injury but things got worse for United when Puncheon - who had just come on- latched on to Damien Delaney's pass to finish past De Gea at the back post against the run of play.
Parity was quickly restored, however, as Rooney surged forward to find the increasingly influential Fellaini.
The Belgian took the ball on his chest and knocked down for Mata to fire home low through the legs of Ward and force extra-time.
Yannick Bolasie went close with a 25-yarder and the dangerous Congolese forward was then felled by Smalling who received his second booking of the match and leave United a man short.
Substitute Dwight Gayle lashed wide and Puncheon again went close, but it was 23 year old local lad Lingard who ensured his place in United folklore with a truly stunning winner.
Antonio Valencia burst forward and saw his cross half-cleared but the ball fell for Lingard to slam home a dipping volley from 20 yards that beat Hennessey all ends up on its way in.
Despite their numerical disadvantage, the Reds held on to that lead fairly comfortably to end a disappointing season on a high and give manager Louis van Gaal the perfect leaving present in an enthralling final.
Overall team performance: 7/10
United Faithful Man of the Match: Wayne Rooney