On Thursday Clattenburg was cleared by the FA over allegations that he racially abused Chelsea's John Obi Mikel during the 3-2 Premier League defeat to Manchester United at Stamford Bridge last month.
The Metropolitan Police had earlier closed their case, launched following a complaint from the Society of Black Lawyers, after no victim came forward.
Professional Game Match Officials Limited general manager Riley, a former ref, said they would record conversations during matches in order to protect officials.
"Regrettably, Mark has had to endure four weeks that have brought massive disruption to his professional and personal life through no fault of his own," said Riley.
"To reduce the risk of an episode of this nature being repeated PGMOL will introduce recording of the referees' communication system on a private basis."
The FA clarified in a lengthy statement that only Chelsea's Brazilian midfielder Ramires had allegedly heard Clattenburg say "Shut up, you monkey" and said six people - three officials using the radio equipment and three players in the vicinity, including Mikel - either did not hear it or were adamant that it was not said.
Chelsea responded thus: "Chelsea Football Club accepts the Football Association's decision regarding Mark Clattenburg and welcomes the fact that the FA recognises the club and players were correct in reporting the matter.
"The club accepts the case is now concluded and notes the FA states the allegation was made in good faith.
"Chelsea FC has a duty of care, as do all employers, to act responsibly when such allegations are reported by employees.
"We did not take the decision to lodge a formal complaint with the FA lightly and followed the correct processes and protocols throughout."
However referees' union Prospect are asking Chelsea for a full apology and compensation on behalf of Clattenburg.
The club have been criticised for failing to apologise to Clattenburg, who also claimed initially that he had abused Spain international Juan Mata.
Respected Daily Telegraph sports writer Henry Winter tweeted: "#cfc fail to apologise to Clattenburg despite making his life a misery with an unfounded allegation. Gourlay's an embarrassment to football" in relation to Ron Gourlay, the Blues chief executive.
The referee has been stood down since the alleged incident, and will not referee this weekend.
The Durham native, who is a FIFA referee and regarded as one of the top officials in Europe, expressed his relief that the case is over.
"To know you were innocent of something but that there was the opportunity for it to wreck your career was truly frightening," he said.
Separately, Mikel has been charged for his behaviour after the match, when he was alleged to have confronted Clattenburg in an angry exchange in his office.
He has accepted the charge and requested a personal hearing.