British Representative Karen Pierce hit back at Nebenzia quoting the Queen in the same novel to ridicule his defence.
"There is another very good quote from 'Alice in Wonderland' which is: 'Sometimes I've believed as many as six impossible things before breakfast'," Pierce said.
"So I think that's the quote the suits my Russian colleague best."
Skripal was a Russian double agent, who also worked for Britain, and was sent there in a spy swap and lived in Salisbury. He and his daughter survived the attack and are recovering in a hospital.
Speaking to reporters earlier on Thursday, Pierce dismissed Russia's demands to be allowed to participate in the investigations with a reference to Professor Moriarty, the arch enemy of Sherlock Holmes, the detective of Arthur Conan Doyle's mystery novels.
"Allowing Russian scientists into an investigation where they are the most likely perpetrators of the crime in Salisbury would be like Scotland Yard inviting in Professor Moriarty," she said.
Russia called for the Council meeting after its bid failed at the Organisation for the Prohibition of Chemical Weapons (OPCW) in the Hague on Wednesday for a joint investigation that includes Moscow into the poisoning probe.
Denying any Russian role, Nebenzia said that blaming his country was a "mega provocation" and he suggested that it was perhaps a "terrorist act".
He raised questions about various aspects of the case, from the survival of the two victims to the time it took for them to fall ill from when they had touched the allegedly poisoned door handle of their home, and from the British official characterisation of Russia's role as "highly likely" to the possibility of the poison Novichok or similar ones being available with others.
By making the allegations against Russia, "we have told our British colleagues that you are playing with fire and you'll be sorry", Nebenzia said.
Later he told reporters that it was also possible that a third country had carried out the attack to create problems for Russia and isolate it by having its diplomats expelled from several countries.
Speaking at the Council, Pierce accused Russia of using a "weapon of mass destruction" on its soil against civilians without regard to public safety.
She said that Britain was carrying out a meticulous investigation that would stand international scrutiny and was cooperating with the OPCW in compliance with the Chemical Weapons Convention.
She also set the attack in Britain in a global context by referring to use of chemical weapons in the killing of North Korean dictator Kim Jong-Un's step brother, Kim Jong-Nam in Malaysia last year and in Syria.
"The threats to the chemical weapons convention from attacks in Syria, in Malaysia, and now the UK pose a serious challenge to the non-proliferation regime," Pierce added.
(Arul Louis can be reached at firstname.lastname@example.org)
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