Clattenburg was cleared last week of racially abusing Chelsea midfielder John Obi Mikel during their 3-2 defeat against Manchester United last month after experiencing what Prospect boss Alan Leighton described as "a living hell" since the allegation was first made.
Villas-Boas saw his side win 3-1 against London rivals West Ham and was pleased to see Clattenburg getting back to his normal duties.
"It was good to see him," he said.
"He is obviously a great referee who has been through a difficult time in his career and he has cleared his name.
"I think for him it was extremely important, he comes back to refereeing on Tuesday or Wednesday and it was good to see him."
Hammers' manager Allardyce echoed the comments of Villas-Boas and is hopeful the situation is now moving towards a satisfactory conclusion for Clattenburg.
"I just said it was good to see him back and get on with your refereeing, nice to see him back. I'm sure he is itching and ready to get back into the middle," he said.
"I don't think it is finally sorted yet but from his point of view he is back where he should be because there is a shortage of experienced, quality referees in our country at least and we couldn't afford to lose him."