The legendary United boss presented Arsene Wenger with a gift in a classy moment before kick-off on what could be the Frenchmans final match as a manager at Old Trafford.
Ferguson and Wenger had a ferocious rivalry before the Scot stepped down at United in 2013 but their differences were put to one side on Sunday afternoon.
Paul Pogba opened the scoring in the 16th minute and the Red Devils were able to keep hold of their lead until half-time.
Henrikh Mkhitaryan came back to haunt his former club in the 51st minute with a well-taken finish from long-range before Wengers party was spoiled at the death.
Marcus Rashford first had a goal disallowed before Fellaini scored a dramatic late winner with a towering header in the 91st minute.
The Sky Sports cameras almost immediately panned to Ferguson and he appeared to be enjoying Fellainis late winner in Fergie time.
Jose Mourinho sent a classy tribute to Wenger ahead of kick-off and urged United fans to be kind to the Frenchman.
He told MUTV: This kind of relationship between a club and a manager is something beautiful and this is the ending of all of this.
Now something like this is not possible anymore so this is the last time he comes here as Arsenal manager. Im sure that us as club he will be welcomed.
I hope also fans can show respect for a man that was Manchester Uniteds rival.
I would say that until 2004 because then there was a power change but for about a decade was about Arsenal versus United.