Ruth Townsley, head of measurement and policy at Bristol-based charity Happy City, took to Twitter to air her views after 32-year-old Paul Crowther threw a milkshake over Mr Farage during a walkabout in Newcastle.
But Ms Townsley sparked outrage after posting a message that appeared to advocate acid attacks and applauded Crowther, who will appear in court on assault charges following the incident.
She said: “Bravo to Paul Crowther, good on you mate.
“Great that milkshakes have become a thing when it comes to the racists in our midst.
“I’d prefer acid but milkshakes will do for now I guess.”
Ms Townsley’s account has since been removed from Twitter and on tuesday Happy City UK issued a statement confirming she had been dismissed from her role.
The charity said: “Happy City is aware that one of their employees poster a tweet yesterday from their personal account about the Nigel Farage protest.
“We do not in any way agree with the contents of that tweet which contradicted all of our strongly held values.
“We believe all politicians have a right to have their voices heard, and condemn violence of any sort at any level of society.
“We are full investigating this incident internally in accordance with out procedures.”
A further statement added: “Ruth Townsley no longer works for Happy City.”
Following the incident Mr Farage said he did not know what was being thrown at him, and called for a message to be sent that "people can't behave like this".
Asked if he would change the way he campaigns, he added: "I hope not but I am concerned about the sheer level of hatred coming from those who think they're better than me.
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"I just think we've reached a point where normal campaigning is becoming very difficult, and that in a democratic society cannot be a good thing."
He said what happened to him was "part of something bigger that's going on".
"Civilised democracy only works if you've got the loser's consent - you know, you lose the election, you don't like it, but you accept it because that's the system.
"Ever since 24 June 2016 we've had senior members of the British establishment - including two former prime ministers - literally refusing to accept the result, saying that those that voted Brexit didn't know what they were voting for - they're thick, they're stupid, they're lazy, they're racist, they're working class, they're fat, they're horrible.
"And that gives people on the other side of the argument a sense of moral superiority. And if you think you're better than everybody else that then leads, I'm afraid, to a breakdown, not just in democracy, but in the civilisation that goes with it.
"And I think we're in a very bad place with this."