The MSP's decision to resign triggers a by-election in the highly marginal Dunfermline seat.
Walker's attempts to blame the media were last night dismissed by Scottish politicians as "a joke".
His position as an MSP had become untenable after he was convicted last month of 23 counts of assault and one charge of breach of the peace.
His conviction came as a result of a Sunday Herald investigation into his violent offences against three ex-wives and a former step-daughter.
Despite his conviction, the MSP initially refused to resign his seat.
Holyrood was powerless to act as MSPs can only be disqualified if they receive a sentence of more than 12 months.
As Walker's case was heard under a summary procedure before a sheriff, the maximum sanction he can receive is 12 months.
His defiance triggered protests outside the Parliament and an unprecedented cross-party call for him to quit, with more than half of all MSPs signing a motion calling for him to resign.
The Parliament also proposed a 90% reduction in salary for any MSP who received a custodial sentence.
Walker's announcement came just hours after the Westminster and Holyrood governments signalled they were ready to work together on a joint solution to disqualify rogue MSPs.
He wrote: "It has been increasingly difficult for my wife and my staff to deal with the media interest in my case. That same media onslaught has also made it impossible to properly represent my constituents and their interests.
"My trial process on domestic abuse charges still continues at Edinburgh Sheriff Court with the sentence not due to be announced until September 20 after the receipt of the reports ordered by the court.
"However, circumstances have made it very difficult to continue as [an] MSP, hence my decision to withdraw now."
Anne Gruber, Walker's second wife, said: "I'm very pleased that he has done the right thing, even at this late stage. Maybe he believes that by resigning he will get a shorter sentence."
Diana Walker, his third wife, also welcomed the decision: "This is fantastic news. I'll be even happier if he gets a full year in jail."
The Dunfermline by-election promises to be a brutal one.
In 2011, Walker won the Labour stronghold for the SNP with a majority of 590 votes, meaning Labour needs just a 1% swing to regain it.
It will be seen as an indicator of SNP popularity going into the last year of the referendum campaign.
Possible contenders for the Labour candidacy include Cara Hilton, daughter of former Falkirk East MSP Cathy Peattie, and Fiona Yates, the daughter of Cowdenbeath MSP Helen Eadie.
Former Lothians MSP Shirley-Anne Somerville has been tipped to stand for the SNP.
The effort to expel Walker increased significantly yesterday after Alex Salmond urged Deputy Prime Minister Nick Clegg to give Holyrood new powers to sanction MSPs.
Salmond said the Walker affair had shown there was an "unanswerable case" for Holyrood having the power to address problems with its own MSPs, rather than relying on Westminster.
The Sunday Herald is campaigning to prevent MSPs with violent criminal convictions remaining in office.
Scottish Labour MSP Claire Baker said: "I am pleased that Bill Walker has finally done the right thing and resigned. The people of Dunfermline deserve better."
Scottish Conservative leader Ruth Davidson said: "There is no place in the Scottish Parliament for people who have committed the crimes that Bill Walker has. It's a disgrace he thought he could hang on and the idea that the media is to blame is a joke. He's a violent misogynist bully."
Jenny Kemp, co-ordinator of the Zero Tolerance charity, said: "We're very pleased that Mr Walker has finally resigned. We've said all along that abusers are not fit for public office."
Scottish Liberal Democrats leader Willie Rennie, who put forward the petition calling for Walker to resign, suggested the SNP should commission an independent inquiry into his election to Holyrood.
He said: "No party is immune from unsuitable people seeking public office using their platform but processes need to be robust to root them out when it is clear who they are.
"The SNP had been told of the allegations about Bill Walker but allowed him to continue to represent them on the council, as a candidate and ultimately in our Parliament."