In the Oxford Dictionary of English Idioms (Oxford University Press – 3^rd edition, 2009), edited by John Ayto, the definition of the phrase the end of civilization as we know it is:

1/ the complete collapse of ordered society;
2/ used to indicate that someone is being alarmist or is overreacting to a trivial inconvenience or blunder as if it were enormously significant and catastrophic.

About its origin, John Ayto writes:

This expression is supposedly a cinematic cliché, and was actually used in the film Citizen Kane (1941): ‘a project which would mean the end of civilization as we know it’.

In Dictionary of English Phrases (Penguin Books, 2008), Robert Allen also writes that the phrase is said to have originated in the film Citizen Kane; he defines it as follows:

The end of a familiar or accepted social order or way of life: often used ironically to question or ridicule an exaggerated view of unfavourable circumstances or setbacks. The phrase is now regarded as a cliché and is associated with science-fiction film dialogues on the theme of attack from outer space.

But the end of civilization as we know it was in use many years before the American film-director and actor Orson Welles (1915-85) made Citizen Kane; the earliest instance that I have found is from The Evening Sun (Baltimore, Maryland) of Thursday 26^th November 1914, which published America And The Allies, itself a reprint of an article about the First World War originally published in The Saturday Review of Politics, Literature, Science and Art (London) of Saturday 7^th November 1914:

Germany put herself hopelessly out of court from the beginning. The Americans, though quick and intelligent in grasping a situation, are not close students of European politics, and they might have been deceived as to the true aims of Germany but for the invasion of Belgium. That was a wrong flagrant and palpable, a wrong no sophistry could obscure. The keen political instinct which the Americans inherit from our common ancestors saw at once that “iron necessity,” once admitted as a principle of international action, meant the end of civilization as we know it.

The second-earliest occurrence of the phrase that I have found is from The Catholic Tribune (St. Joseph, Missouri) of Saturday 6^th September 1919, which published an interview of Frank P. Walsh, “former joint chairman of the National War Labor Board, who for many years has been one of the most widely known advocates of the rights of labor”:

“The fight between the labor unions and the employers for the last quarter of a century has been a struggle for mastery of man over man. The employers declare, ‘No man or set of men can tell us how to run our business.’ The workers, where they have attained collective voice, declare, ‘No men [sic] or set of men can control our lives.’ So the world, including our own country, has come to an impasse—for the workers have grown strong enough to paralyze the basic industires [sic] almost at will. The consumers’ day is here. The rights of the public—which term means all the workers and employers—are declared paramount. This means an end to this wasteful struggle for mastery. There must be willing cooperation, with full, hearty joint control by workers and employers in all basic industries or an end to civilization as we know it.”