Crawley and their 9,000 travelling fans headed home with an aching sense of a chance missed as Wes Brown's first-half header proved enough to give United an unconvincing fifth-round victory at Old Trafford on Saturday evening.
A defiant display from the proud non-leaguers nearly gained its just reward when Richard Brodie guided a stoppage-time header onto the top of the crossbar.
The hosts survived though, despite being so poor, ending the game with Rooney and Javier Hernandez occupying wide positions, either side of an ineffective Gabriel Obertan and an anonymous Bebe.
Indeed, Rooney's frustrations bubbled over into a cynical lunge on Kyle McFadzean that earned the England striker a yellow card.
It will be of no consolation to Crawley that Brown's header was a collector's item. His first goal since October 2008 and only his fifth in over 350 games for the Red Devils.
The Blue Square Premier promotion contenders started brightly and grew in confidence as the contest went on, their valiant push for an equaliser gathering momentum with each passing minute.
If it was not a surprise Brown was named in Ferguson's starting line-up, it was a shock he received the captain's armband ahead of central defensive partner John O'Shea.
The 31-year-old has drifted out of the first-team picture since he featured in the 2008 Champions League final, to the extent this was only his 11th appearance of the season.
Indeed, he was tipped to leave Old Trafford during last month's transfer window and given the performances of Chris Smalling this season, his future beyond the end of this season is uncertain to say the least.
However, Brown can always be relied upon to give everything in the United cause.
Goals have never been part of his repertoire. But with United's second-string outfit struggling to turn their possession into something more tangible, he led from the front.
Darron Gibson had just picked out Javier Hernandez with an excellent pass that led to a corner.
Gibson drifted the ball over from the left touchline, Brown leapt highest, and the faintest of touches took it past Michel Kuipers and into the bottom corner.
The hosts should have doubled their lead before the interval.
Gibson's defence-splitting pass to Fabio left the Brazilian to race through on Kuipers' goal.
However, he prodded the ball with his right foot instead of shooting with his left and the end product rolled disappointingly wide of the target.
A second goal would have been harsh on Crawley though.
Their performances so far this season have led Ferguson to predict Crawley will be in the Football League next term.
The money being thrown at the aim has not won favour with all their rivals, with plenty questioning exactly where it is coming from.
However, this represented the biggest day in their history given Manchester United are on a different scale altogether.
Had Ben Smith's 30-yard strike been on target, it might have given them a shock lead too.
Unfortunately for the visitors, it dipped narrowly wide of a goal being manned by Anders Lindegaard, who was making his home debut.
The introduction of Rooney at the break indicated Ferguson was not entirely satisfied with what had gone before.
Chris Smalling's arrival in place of Rafael 10 minutes after the re-start was a statement of the dominance Crawley enjoyed in that period, even if O'Shea's stout defending kept them at arm's length.
Rooney had barely touched the ball but eventually he advanced into a shooting position, even if he was unable to keep his 20-yard effort on target.
By that point though, Crawley had realised there was nothing to fear and attacked in the same manner they will probably do against Southport on Tuesday.
Hunt got on the end of Brodie's cross and flashed an effort just wide, then, aiming for the same goal Rooney found in such spectacular fashion seven days earlier, Matt Tubbs' overhead kick sailed narrowly over.
There was one chance left, which Brodie was unable to take, failing to provide the perfect end to a dream day.