As the captain and match-winner Cantona walked up the 39 steps to collect the Cup from the Duchess of Kent, he was spat at by one fan wearing Liverpool colours. And Ferguson, the Manchester United manager, avoided a punch thrown by another spectator.
While both men played down the incidents, the Football Association, with its sights fixed firmly on next month's European Championships, immediately launched an inquiry.
The FA chief executive, Graham Kelly, said: "It was totally unacceptable. I am very concerned about the situation and we will be reviewing the matter urgently with Wembley.
"Clearly there was a problem with players walking past rival fans. I have already spoken to Wembley and we will be looking at the matter in some depth."
Ferguson dismissed the incident as "silly", adding: "If someone had a swing at me he obviously doesn't know how good I am at fighting."
Cantona, who turned to stare at his assailant before continuing up to the Royal Box, played it down as well.
"It was not a problem as far as I am concerned," he said. "I know there is rivalry between Liverpool and Manchester United, that there can be trouble, but it didn't matter to me."
Martin Corrie, a Wembley spokesman, said that efforts would be made to identify the culprits.
"We had cameras trained on that area and know who should have been in which seats," he said. "We are concerned at what was a distasteful incident and can use that visual reference to hopefully identify the people involved. If we can do that, then we will consider what further steps we should take against them."
Manchester United fans threw a giant street party when their team returned home yesterday. An estimated 100,000 people lined the team's triumphant route through the south of Manchester, cheering their open-topped bus as it drove two and a half miles through a sea of noise and colour. French tricolours in honour of Cantona outnumbered the more traditional red, white and black of United.