While quintessential means 'representing the most perfect or typical example of a quality or class' [OED], it defines essential as 'absolutely necessary; extremely important'. I have noticed frequent instances of the two being used interchangeably. How did this come about?
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I don't think they are even near to one another and even if someone comes across their cross reference it's should be considered a mistake.
All one can correlate between the two words is :-
Note: Though quintessential has it roots in medival latin which points towards aether [the classic element also known as fifth element(after earth, fire, water, and air)] but to the end that too points towards achieving the purest essence, of one which heavenly bodies are composed.[reference link]
Also through the course of language and literature its meaning has kept on evolving following to current definitions along with their usage examples.
To further narrow down the ambiguity here is a brief article on etymology of the same.
Different borrowings, and different metaphors.
Essence is from Latin essentia 'essence, being'.
Quintessence comes from Mediaeval alchemical Latin, for quinta essentia 'fifth essence', meaning a potion that had been distilled five times. So it probably means being that's a hundred proof or more; i.e, it's an intensifier, like very. But since essence is so immaterial, there's no real difference between the meanings. Quintessence is a learned word, but that may or may not matter.
I researched this question in hopes to find an easy answer, but I came away more puzzled than when I started.
Here are the synonyms of essential suggested by my computer's on-board thesaurus (sure enough, there is quintessential, listed among the candidates), followed by the definitions provided by its dictionary:
There are two oddities, at least in my mind. First, I can't find anything in the meaning of essential that carries the essence of quintessential; second, when I looked up the other synonyms for essential in the thesaurus (i.e., when I looked up basic, inherent, fundamental, intrinsic, underlying, etc.), they all listed essential as a synonym in the reverse direction. As can be seen by the bottom part of my screenshot, though, essential is conspicuously missing from the listed synonyms of quintessential.
This leads me to believe that using quintessential in place of essential would be a mistake, as Raghav said in an answer, and Kate Gregory mentioned in a comment. Yet it's not too often that such a "mistake" would be supported by a thesaurus.
I even looked up essential and essentially in the OED, as Tim Lymington suggested, and still couldn't find any clear-cut link.
Since I was unable to find a satisfactory answer to your question, I feel compelled to upvote it; it is a quintessential etymological puzzler.
Have a look at this:
suggesting that we don't see the words crossing each other, hence I would suggest they have not yet been replaced as yet. Besides in short, essential means indispensable, while quintessential means the most typical. And Thesaurus.com does point out quintessential as a synonym of essential, supporting what you mentioned in your original post, but I guess its like saying I always procrastinate my work then saying I always delay my work until the end.