The Derby North MP was suspended in February after he claimed that Labour had been "too apologetic" in response to criticism of its handling of anti-Semitism allegations.
He was readmitted to the party and issued with a formal warning following a hearing of a National Executive Committee (NEC) anti-Semitism panel in June - prompting an outcry from MPs, peers and Jewish groups.
But he was suspended again in July after a second panel reviewed the decision to reinstate him and found it "cannot safely stand".
Labour also imposed a separate suspension on September 3 over additional allegations of misconduct.
At a hearing in September, Mr Williamson’s lawyers argued that his treatment had been "manifestly unfair" and asked the High Court to declare his suspension from the party was void.
Giving judgment on Thursday, Mr Justice Pepperall ruled that "the Labour Party acted unfairly in that there was no proper reason for reopening the case against Mr Williamson".
However, the judge found that there was "nothing in the new allegations, the timing of the letter of 3 September or the decision to suspend that entitles me to take the view upon the papers that the Labour Party is acting either unfairly or other than in good faith".
He added: "I therefore refuse relief in respect of Mr Williamson’s recent re-suspension. The new disciplinary case must run its course."
In his ruling, Mr Justice Pepperall stated: "It is important to stress at the outset of this judgment that this case is not about whether Mr Williamson is, or is not, anti-Semitic or even whether he has, or has not, breached the rules of the Labour Party.
"The issue is whether the party has acted lawfully in its investigation and prosecution of such charges against Mr Williamson."
In a statement issued by his lawyers after the ruling, Mr Williamson criticised Labour’s disciplinary procedures and called on the party to lift his suspension.
He said: "I welcome the court’s recognition of the unfair manner in which I have been treated by the Labour Party in this process.
"I have been a member of the Labour Party for almost 44 years and I have had the privilege of serving in elected office for my party for over 28 years, first as a councillor and then as a Member of Parliament.
"I never expected, nor wanted, to be in a position where I was forced to take legal action against the party to which I have devoted my life.
He added: "I've spent my life fighting racism, right from being a young man, when I was working on the building sites in Derby when racism in the 1970s was prevalent and I risk my personal safety to challenge racism in the working site."
"It is absolute calumny and a disgrace that anyone should accuse me of anti-Semitism."
He said: "I will continue to fight to clear my name and also on behalf of others that have suffered, or who in the future suffer injustice in the Labour Party disciplinary process."
A Labour Party spokeswoman said: "The court has upheld Chris Williamson’s suspension from the party and has said his disciplinary case must run its course."