"The events of Charlottesville alerted us to the need for immediate action."
"We want you Nazis to know: Your time is short" it said, using the hashtag #Tangodown.
The group said "hackers of the world have united in defence of the Jewish people. You should have expected us".
It vowed to leave the site live for 24 hours before shutting it down permanently.
The cyber attack comes following large protests across the US against fascism and racism after Heather Heyers and two others were killed at a protest in Charlottesville, Virginia where white supremacist groups clashed with counter-protesters.
Heyers was struck when a car drove at speed into a group of anti-racism protesters. Her friend, Marissa Blair called it an "act of terror" as the driver "barrelled down" and accelerated.
Twenty-year-old James Alex Fields Jr. is charged with second-degree murder and other counts in the car crash. He could also face federal charges, depending on the outcome of an FBI investigation.
The Daily Stormer had previously advertised an "ignite the right" protest for Saturday in Charlottesville with the slogan "you will not replace us".
Anglin live-blogged the weekends events and encouraged those in Charlottesville to "go out and enjoy yourselves" after the events.
"This was a weird day, a historic day, and day on which all things have been permanently change," he wrote. "And it is mostly change for the better.
"If you're at a bar in a group, random girls will want to have sex with you. Because you're the bad boys. The ultimate enemy of the state. Every girl on the planet wants your dick now."
He also warned people they are "now at war".
"There will be more events. Soon. We are going to start doing this non-stop. Across the country. I'm going to arrange them myself. Others will too, I'm sure, but I'm telling you now: I am going to start arranging my own events. We are going to go bigger than Charlottesville. We are going to go huge."
Social media users praised Anonymous for their actions under what they have dubbed "OpKKK" and "OpResistance".
The shocking events have led to criticism of President Trump for failing to condemn white supremacist groups or label the killing an act of terror.
Trump's initial response to the crisis was to condemn violence "on many sides".
A new White House statement on Sunday explicitly denounced the Ku Klux Klan and neo-Nazi groups, but it was attributed to an unnamed spokesman and not the president himself.
"The president said very strongly in his statement yesterday that he condemns all forms of violence, bigotry and hatred and of course that includes white Supremacists, KKK, neo-Nazi and all extremist groups," it said.
Trump's national security adviser, H.R. McMaster, said Sunday that he considered the attack to be terrorism. On Saturday, Trump had not responded to reporters' shouted questions about terrorism.
"I certainly think anytime that you commit an attack against people to incite fear, it is terrorism," McMaster told ABC's "This Week."
"It meets the definition of terrorism. But what this is, what you see here, is you see someone who is a criminal, who is committing a criminal act against fellow Americans."
