Clattenburg was cleared this 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.
Spurs boss Andre 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 Sam 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."
Leighton, the national secretary of the referees' union, reckons Chelsea's handling of the complaint against Clattenburg could prove a step backwards in the fight against racism in football.
Chelsea based their complaint on what Brazilian midfielder Ramires thought he heard, and the club have been criticised for making the allegation against Clattenburg public from an early stage.
Prospect boss Leighton believes the case could dissuade players from reporting instances of racial abuse in the future.
He told BBC Radio Five Live's Sportsweek programme: "We think this is the wrong way to go about combating racism, and in fact what Chelsea have done could put people off making legitimate claims when they have been subjected to racial abuse.
"It's been terrible for him, he's been through a living hell. He's had the press camped on his lawn.
"He's had to live with walking down the street and people either pointing at him or him thinking people are thinking, 'Oh, that's the racist referee'.
"Everybody always remembers an allegation but not everybody always remembers the outcome."
Chelsea have so far made no apology to Clattenburg for his ordeal, and noted in their statement earlier this week that the Football Association felt the complaint had been made in good faith.
Leighton believes Clattenburg wants to avoid a legal battle and get on with his job, and he added: "If Chelsea want to make an apology, pay compensation and get Mark to sign an agreement saying he won't take legal action, I'm sure we can do that."
Meanwhile, Leighton hopes it is not too long before Clattenburg takes charge of another Chelsea game.
"I think if there was too long a delay in refereeing Chelsea then I think the issue gets dragged out again," he said.
"The key issue for Mark is getting back to refereeing and getting back to normal, and that means refereeing Chelsea as soon as he possibly can."
Clattenburg will take charge of Southampton's Barclays Premier League clash with Norwich on Wednesday evening, his first game back as referee since the allegations first surfaced.