Mr Murdoch’s wife, Wendi Deng, who was sitting behind her husband, leapt to his defence as the man, wearing a checked shirt, tried to hit the media mogul with the pie.
His son, James, who was sitting next to him during the Culture Committee evidence, also jumped up to defend his 80 year-old father.
The protest was seen live on television and the internet. The man was heard shouting: “I got him.”
Mr Murdoch was left with foam on his clothing.
The protester was seen being held by police with foam his face and clothing.
It will lead to inevitable questions over the security operation surrounding the Murdochs’ appearance in Parliament.
The dramatic events led the hearing to be suspended just before 5pm and began again around 15 minutes later.
Earlier, Mr Murdoch, the Chairman of News Corporation, told MPs that he does not accept responsibility for wrongdoing at the News of the World.
He told a committee of MPs investigating phone hacking: “I do not accept ultimate responsibility. I hold responsible the people that I trusted to run it and they people they trusted.
He earlier said he was appalled when he heard that reporters had hacked into the voicemails of missing teenager Milly Dowler.
A contrite Mr Murdoch today appeared before MPs and declared: “This is the most humble day of my life”.
Sitting alongside his son, James, the 80-year-old media mogul said that he was “more than prepared” to answer the questions of the Commons Culture, Media and Sport Committee into the phone hacking scandal.
James Murdoch, News Corp’s deputy chief operating officer, opened by saying how sorry he and his father were to the victims in the News of the World phone-hacking scandal.
“It is a matter of great regret of mine, my father’s and everyone at News Corporation. These actions do not live up to the standards our company aspires to everywhere around the world,” he said.
“It is our determination both to put things right, make sure these things don’t happen again, and to be the company that I know that we have always aspired to be.”
James Murdoch told the committee the company acted “swiftly” as soon as it became aware of fresh evidence over phone hacking following a series of civil actions in 2010, particularly the case involving actress Sienna Miller.
It became apparent that more people than originally believed were victims of the practice, he added.
Mr Murdoch Jnr said: “Subsequent to our discovery of that information in one of these civil trials at the end of 2010, which I believe was the Sienna Miller case, the company immediately went to look at additional records around the individual involved, the company alerted the police and restarted, on that basis, the investigation that is now under way.”
He said the company had apologised “unreservedly, which I repeat today,” to phone hacking victims.
He added: “The company acted as swiftly and transparently as possible.”
Asked by Labour MP Tom Watson whether he had been “misled” by senior employees, Mr Murdoch senior replied: “Clearly.”
Mr Watson pointed out that former News International chief executive Rebekah Brooks admitted in 2003 that police were paid for information.
Mr Murdoch senior said: “I am now aware of that, I was not aware at the time. I’m also aware that she amended that considerably very quickly afterwards.”
Mr Watson said: “I think she amended it seven or eight years afterwards but did you or anyone else in your organisation investigate it at the time?”
Mr Murdoch replied: “No. I didn’t know of it.
“I’m sorry, if I can just say something and this is not as an excuse, maybe it’s an explanation of my laxity.
“The News of the World is less than 1% of our company. I employ 53,000 people around the world who are proud and great and ethical and distinguished people, professionals in their work.
“I’m spread watching and appointing people whom I trust to run those divisions.”
Mr Yates said the Met turned over a “huge amount of staff”, many on short-term contracts.
“There are numerous examples from numerous senior people, both within the Metropolitan Police and Metropolitan Police Authority, where people who are known to those people have been employed on a short-term basis and some have even become permanent employees. So it is not unusual.”
Mr Yates said he classed Mr Wallis as “a friend”, but stressed they were not “bosom buddies”.
“I must have been round there once to pick him up for a football match. I would see him maybe two or three times a year,” he said.
“Do not get the impression that we are the bosom buddies, living in each other’s houses.”
Mr Yates insisted he had not carried out “due diligence” when Mr Wallis was given the Met contract, and had only sought “assurances” that there was not anything being chased by the Guardian that was going to embarrass “him, me, the commissioner or the Metropolitan Police Service”.
The assistant commissioner was asked about Sir Paul’s reference to a No 10 official who recommended they should not disclose information such as Mr Wallis’s links to the Yard to the Prime Minister.
Mr Yates said that last September he emailed Downing Street chief of staff Ed Llewellyn offering to brief Mr Cameron on aspects of the hacking inquiry.
“There was an offer in the early part of September 2010 for me to put into context some of the nuances around police language in terms of what a scoping exercise is, what an assessment is…
“That offer was properly and understandably rejected.”