Zheng Xiyuan and five of his staff had already departed from the UK or would do so shortly, the Foreign Secretary told the Commons.
They left or were going after the Foreign Office asked Beijing to waive their immunity so they could be interviewed by police in Manchester about the incident, he added.
The Chinese authorities were given one week to “comply” with the request.
“In response, the Chinese Embassy, acting on instructions from Beijing, notified His Majesty’s Government that the functions of the Consul General in Manchester have come to an end and he has returned to China,” said Mr Cleverly.
“The Embassy has further notified us that the other staff involved in the incident who the Police wish to interview have either left the United Kingdom or will shortly do so.
“I am disappointed that these individuals will not be interviewed or face justice.
“Nonetheless, it is right that those responsible for the disgraceful scenes in Manchester are no longer – or will shortly cease to be - consular staff accredited to the UK.”
Greater Manchester police launched an investigation in October after social media images showed “what appeared to be completely unacceptable behaviour by a number of individuals near the entrance to the consular premises,” he added.
The footage appeared to show a Hong Kong pro-democracy protester being dragged inside the grounds of the diplomatic mission and assaulted.
The Foreign Secretary said: “The right of free expression - including the right to protest and to speak one’s mind - is absolutely essential to our democratic life.
“We have been clear with China from the outset that we were prepared to take firm action should the police determine that there was a case to charge officials for their involvement in the incident.”
He added that a “certain standard of behaviour” was expected from all foreign diplomats and consular staff “regardless of their privileges and immunities”.
The Vienna Convention on Consular Relations allows States to withdraw members of a consular post at any point, even if they face a possible police probe.
1. Relations between Britain and China have hit new lows recently, with Rishi Sunak declaring that the ambition to create a “golden era” of relations with Beijing is over amid the concerns over the country’s human rights record, president Xi Jinping’s authoritarian regime and its military and foreign policy aims, and its spying operations.
2. Responding to Mr Cleverly’s statement, Alicia Kearns, the chair of the Commons Foreign Affairs Committee, said: "The people of Britain rightly expect those who commit crimes on our shores to face the consequences. That is what it means to live in a country with the rule of law.
3. "The Foreign Office must now declare those who have fled persona non grata, and make clear they are never again welcome in the UK."
4. The decision of the Consul General and the other staff to be withdrawn by Beijing, rather than expelled if they were found to have committed any crimes, means that a tit-for-tat response from China is less likely.