The East Renfrewshire MP said he was awaiting advice from Police Scotland as well as promises by the hierarchy of the Yes campaign that they would "call off the attack dogs" before starting the tour again.
But the former UK Government minister has been accused of attempting to blacken the entire independence campaign and "scare people away from the debate", with Yes Scotland saying it "condemns all forms of abusive, dangerous and offensive behaviour".
The decision came less than 24 hours after he was hit by an egg while speaking in Kirkcaldy.
It also follows reports that First Minister Alex Salmond called in police after being chased in his official car by a motorist waving a No sign, and said politicians should not seek to take advantage of protests and hecklers.
Prime Minister David Cameron also claimed yesterday that people who threw things at politicians had no place in the democratic process.
Mr Murphy, who claimed he had been challenged to a fight in Aberdeen and described his hecklers as "nationalists mobs", said: "The blame lies at the door of Yes Scotland. They should stop this intimidation."
Mr Murphy insisted his decision to publicise the suspension and show videos of hostile crowds at his shopping-precinct debates was "not about showing your opponents in the worst possible light".
But he claimed disruption of his events in recent days was being pulled together officially by Yes Scotland, claiming they had in one instance been gathering at the campaign's local headquarters and publicising his tour on Yes Facebook pages.
He said many of those involved in recent disruption of his street meetings, of which more than 80 have been completed, had been following his tour to various stop-offs, putting a total figure of those involved in the hundreds.
Mr Murphy also claimed the antagonism was one-way and that there was no equivalent of such abuse directed against the Yes campaign.
He added: "We are not going to be silenced and intimidated by a noisy nationalist mob.
"We would never dream of co-ordinating this type of activity. What is it they think they are trying to achieve? Undecided voters are shocked and turned off by it. All I can ask is to call the mobs off."
The tour has 18 more stop-offs and was due to include the Borders, Edinburgh and East Lothian in the coming days. Mr Murphy said he would consider whether to press charges against the heckler who hit him with the egg after speaking again to police.
One senior Better Together source said Mr Murphy had gone public through a duty of care to his staff and said he hoped the appeal to Yes Scotland would halt such protests rather than fuel a spiralling trend of retaliation and recriminations.
But Robin McAlpine, of the Radical Independence group, said: "There's a tiny number of people on either side behaving badly. There's numerous examples of No campaigners being aggressive and damaging the property of Yes campaigners.
"But we don't press-release this or make a big deal because we don't want to scare people away from this.
"This has been a thoroughly positive and uplifting debate and the No campaign obsession with unrepresentative issues speaks only to their lack of confidence in their cause."
Glasgow SNP MSP James Dornan said: "It's the exact opposite of being co-ordinated. It is people at the margins of the campaign. Let's not pretend this is what the Yes campaign is about. It's a peaceful, respectful, democratic campaign."
A Yes Scotland spokesman said: "We condemn all forms of abusive, dangerous and offensive behaviour, whether it be Jim Murphy having eggs thrown at him, or Alex Salmond being harassed by a road-rage motorist.
"For the most part, the independence debate has been conducted in a responsible, peaceful and enthusiastic manner with only a very small minority on both sides behaving badly."
l A man has been found guilty of posting threatening comments on the microblogging site Twitter in which he threatened to assassinate the First Minister.
Christopher Stevenson, 26, posted: "Think I might assassinate Alex Salmond" while watching a TV programme about him.
An American visitor to Scotland saw the message on the social networking site and contacted the police.
Fire safety security technician Stevenson from Alexandra Gate in Glasgow's east end told police it was a joke but was convicted after trial at Glasgow Sheriff Court of behaving in a "threatening or abusive manner which was likely to cause a reasonable person to suffer fear or alarm".
Sheriff Graeme Warner deferred sentence on Stevenson for a year for him to be of good behaviour.