The deputy prime minister accused the Ukip leader of "insulting" the Kiev uprising and said he would have to explain why he was "siding with Vladimir Putin".
As the two politicians went head to head in a live debate, Farage said the British Government had encouraged the EU to pursue an "imperialist, expansionist" agenda.
Protesters took to the streets of Kiev following the decision of president Viktor Yanukovych's decision to reject an association deal with the EU, preferring closer ties with Russia, with dozens killed in the violence.
Following his loss of power, the Russian-leaning Crimean peninsula has been effectively annexed by Moscow and there are fears that President Vladimir Putin could make a move on the country's eastern regions.
"We should hang our heads in shame," Farage said on LBC Radio. "We have given a false series of hopes to a group of people in the western Ukraine and so geed up were they that they actually toppled their own elected leader. That provoked Mr Putin, and I think the European Union, frankly, does have blood on its hands in the Ukraine."
Clegg, asked about the comments during his weekly phone-in on the station, condemned his rival's response.
"It shows quite how extreme people can be like Nigel Farage when their loathing of the European Union becomes so all-consuming that they even end up siding with Vladimir Putin in order to make their point," he said.
"To suggest that somehow it is the European Union's fault that the Ukrainian people rose up, as many did on the streets of Kiev, against their government - seeking to claim greater democracy, greater freedom - it is such a perverse way of looking at things.
"What Vladimir Putin has done and what the Russians have done, in effect annexing a part of another country in the heart of Europe, is simply unacceptable in this day and age.
"The only reason we are able to seek to exert any influence - and it is difficult enough as it is - on Vladimir Putin is because we can act with the clout of being part of the economic superpower that is the European Union, upon which Russia depends a lot."
He went on: "It is really insulting to those people who, in Kiev, were simply standing up for values which we should share and support, of democracy, autonomy, of them being able to determine their own fate.
"For Nigel Farage to side with Vladimir Putin, he will have to explain why he did so. I was astounded. It was in many ways the most striking, if not shocking, new revelation that came to light."
Clegg was joined in his criticism by the Conservative cabinet minister Andrew Lansley. The leader of the Commons told MPs on Thursday morning: "I am staggered, I think its outrageous that Ukip should be behaving as apologists for Putin."