Manchester United holds off Fulham
Rooney paid the price for a below-par performance in the defeat at Everton on Monday.
It is a reminder from Ferguson that standards have to be higher.
And the respective performances of Van Persie and Kagawa were such that Rooney would not have been guaranteed a recall at Southampton next week.
However that will not happen now, after sustaining a nasty gash in stoppage time after being trodden on by Hugo Rodallega - an incident which left United to play out the game with 10 men and Rooney out for four weeks.
Before then a week of frenzied transfer activity is due, with Rooney's name doubtless being mentioned, in addition to Nani, who did not even merit a place on the bench.
Ferguson is more concerned about points, which were collected as the first-half response of Van Persie, Kagawa and Rafael to Damien Duff's second-minute effort proved enough despite a Nemanja Vidic own goal.
Rumors swept Old Trafford that Rooney had been axed long before official confirmation was received an hour before kick-off.
It is not the first time the England striker has suffered such a fate.
On New Year's Eve last season, Ferguson omitted the 26-year-old for disciplinary reasons against Blackburn - a decision that proved very costly as the Red Devils suffered a home defeat against a team that went on to get relegated.
Yet there was never any suggestion Rooney would be left out for the long term.
However, as he made his way to the home dressing room after witnessing a powerful first-half display from the hosts, in which Ferguson's two big summer signings both opened their United accounts, Rooney must have had a worry or two.
For in addition to their goals, Van Persie and Kagawa in particular caught the eye with how easily they fitted into the system.
Kagawa excelled in the hole behind the main striker. His movement, speed and passing kept Fulham on the back foot. And this, shrewd judges from Japan insist, is his best position.
So to where in that, would Rooney fit? It gave a different view to Ferguson's program notes, in which he said that anyone who had "fallen out of love" with the club he would "invariably help them on their way out".
That is not to say such a fate awaits Rooney.
However, it is worth noting Jaap Stam featured in United's first game of the 2001-02 season, against Fulham of all teams, and was promptly shown the door.
Not that Ferguson's brave move had a particularly impressive start as Bryan Ruiz rolled a free-kick into Duff's path which the Irishman turned home before guest of honour Usain Bolt had even taken his seat.
Coming so soon after that loss at Everton, it was a major test of character for United which they came through with flying colors.
Van Persie levelled with the clinical efficiency you would expect of a Golden Boot winner.
Meeting Patrice Evra's left-wing cross perfectly, the Dutchman flashed a shot wide of Mark Schwarzer before turning to receive the acclaim of his team-mates.
From that point on it was a case of when, rather than if, the hosts would gain the initiative. As Kagawa prompted and cajoled, Ashley Young and Antonio Valencia both went close.
But when Van Persie's corner was half-cleared to Tom Cleverley, Schwarzer could only turn the midfielder's shot into the path of Kagawa, who - profiting from Sascha Riether's failure to get out of the six-yard box quickly - swept home from close range.
Restored to the starting line-up following his Olympic campaign with Brazil, Rafael provided additional defensive security.
He also had a goal correctly ruled out for offside before nodding home Young's chip to the far post just before the break.
Yet, for all United's attacking endeavors, there remain serious flaws at the back amid a massive injury list. Once again pressed into service as an emergency center half, Michael Carrick came far too close to turning the ball into his own net for comfort.
And when United conceded a second, it was almost laughable as David de Gea came to punch Matthew Briggs' cross, got nowhere near it and the ball eventually bounced off Vidic and rolled in.
De Gea redeemed himself with two brilliant saves to deny the excellent Mousa Dembele as Rooney was introduced for Kagawa.
And then, on Fulham's last attack, De Gea denied Ruiz, who had been set up by Dembele.
Information from The Associated Press was used in this report.