Ferguson was present in the directors' box for the first time since his retirement in May after recovering from a hip operation.
And the Scot was watching on as Rooney stamped his mark on a comfortable afternoon for United, netting his first goal since March 10 minutes from time after Robin van Persie had put the hosts ahead with a controversial penalty just before the interval that led to Kagisho Dikgacoi's dismissal.
It represented David Moyes' first victory at the stadium he now calls home and, after two games without a win, allows him to approach a significant week in confident mood as United face Bayer Leverkusen in the Champions League on Monday before next Sunday's Manchester derby at the Etihad Stadium.
Had Ferguson remained in his job, it is hard to see how Rooney would have still been at the club such was the deterioration in their relationship. It is the Scot's presence in the background that is said to have made the striker think so hard about his future.
With the transfer window closed there can be no more talk of Chelsea, or anyone else for that matter.
And typically in such circumstances, Rooney is able to concentrate fully on his football which is, after all, what he is best at.
Sporting a rather strange cushioned head band to protect the wound inflicted by Phil Jones immediately prior to the international break, at long range Rooney looked a bit like a Roman emperor.
He was certainly a source of goals though and it was Rooney's long ball over the Crystal Palace defence that Van Persie cushioned on his chest, then crashed against the crossbar.
It was the best chance United had created up to that point, their opportunities being limited to long-range strikes from Michael Carrick, Fabio - on his first league start since November 2011 - and Rooney, only the first of which tested Julian Speroni.
It is not that long ago since Ferguson was defending Ashley Young against allegations of diving.
Now Moyes has to address the issue after the England winger was booked for going down twice under pressure from Dikgacoi.
On the first occasion, Young clearly sought contact and merited the yellow card dished out by referee Jon Moss.
The second instance was far less clear cut. Some felt Young initiated the brush against the Palace midfielder that ended with him sprawling inside the box.
Had Moss felt the same way, Young would have been off. Instead it was Dikgacoi making the sad walk to the dressing room as the referee decided the South African was responsible.
After almost two-and-a-half games without a goal and having just survived a major scare when Dwight Gayle got round the blind side of Rio Ferdinand and clipped a shot narrowly wide, United were not in a position to be picky.
Van Persie kept his nerve and sent Speroni the wrong way.
The goal did not quite release United's shackles but they did start to exert pressure with more conviction.
Young came close twice, then cut the Palace defence apart with a superb through ball to Patrice Evra, whose intelligent cut-back was not read by any of his team-mates.
Antonio Valencia picked out Rooney on the other side of the box, but the England man's control let him down.
When Van Persie ballooned United's next chance over, Moyes introduced Fellaini, followed not long afterwards by teenager Adnan Januzaj.
Both wasted little time in making an impact as Januzaj ghosted into the box to create uncertainty in the Palace defence, which Fellaini almost exploited with a powerful shot Speroni kept out with his knees.
Januzaj then provided the pass from which Van Persie rifled over before going on to tease the visitors in much the same way as Cristiano Ronaldo did on roughly the same patch of turf when he made his United bow against Bolton a decade ago.
Van Persie brought another save out of Speroni from an acute angle before Januzaj was brought down on the edge of the box and Rooney stepped up to curl the free-kick into the bottom corner.
Rooney looked rather pleased with his efforts and, if nothing else, it does seem the summer controversies are behind him.