Because the noun car is modified by the superlative adjective best, and because this makes. It is also a superlative, like greatest, or highest, so just as you would use it as an adjective to show that something is. Your example already shows how to use best as an adverb.
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In the following sentence, however, best is an adjective:
Which one is the best is obviously a question format, so it makes sense that which one the best is should be the correct form.
This is very good instinct, and you could. You could certainly declare that after. What was best? if we insert the word the, we get a noun phrase, the best.
