Clattenburg had been accused by Chelsea of making a racist remark to John Obi Mikel during a game with United at Stamford Bridge last month. There have been calls for Chelsea to apologise and the club are understood to be considering how to respond.
Ferguson, who had spoken up for Clattenburg in the immediate aftermath of the allegation, said: "I did not believe it anyway. The unfortunate thing for Mark is that he has had to carry that stain for the last few weeks. Everyone in the game is pleased for him now - apart from Chelsea."
Former Premier League official Graham Poll does not see a reason why Clattenburg will not be able to referee a Chelsea game again in the future.
Poll himself was subjected to accusations from some of the London club's players in 2006, with allegations he said he had promised to "sort them out" later withdrawn.
"I don't think, given time, we will have a situation where Mark Clattenburg can't referee Chelsea," he told talkSPORT.
"Mark won't have a problem with the players at all. They truly believed Ramires had heard something improper from the start. You can understand the strong feeling, and the fact that it was misinterpreted is not the problem."
Poll criticised Chelsea for making the allegation known, adding: "The issue is Chelsea Football Club. I understand they have to investigate the allegation and protect their employee.
"But they went so public and were so damning before they had looked at it first. That's the issue."
Aston Villa manager Paul Lambert also believed Chelsea should not have made their complaint public. He said: "Was it right to go public on the issue? I would say no. Anything like that should be handled behind closed doors."
Source: PA
Source: PA