Although запятая is a noun, its endings make it look like an adjective, so I presume that there is some implicit noun that запятая is modifying without ever being explicitly used (similar to столовая = столовая комната and кривая = кривая линия). What is that noun?
2 Answers
It's a nominalized adjective (similar to forms мороженое, жаркое etc.) derived from the CS word запѧти (to stop). So запятая means "stopped".
Most probably, it modified the word боукы (буква in modern Russian, meaning "letter").
The Russian word препинание (as in знаки препинания, "punctuation") derives from the same root.
Unlike most CS and Russian linguistic terms, it's not a calque from a Latin or Greek term, which means the term appeared very early (late XV or early XVI). Zizany and Smotritsky both mention it in their grammars.
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1you are wrong, comma in russian punctuation is relatively new. Moreover, at the very beginning it hadn't called "запятая". Here is an interesting article on the subject - philolog.pspu.ru/module/magazine/do/mpub_10_180– shabunc ♦Commented Oct 3, 2012 at 9:16
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1@shabunc: I am speaking about the term, not the sign itself. "Early" here means Maximus the Greek or the same time, before him Russian and CS lacked linguistic terms on their own at all. Zizany and Smotritsky mainly calqued Latin and Greek terms.– Quassnoi ♦Commented Oct 3, 2012 at 9:20
Word запятая is derived from verb запинаться as
запинаться-(запинать)-(запять)-(запятóй*)-запятая
(Note that the words in parentheses do not exist in the modern Russian language.)
As such, it is closer to an adverb rather than an adjective. There is no implicit noun in this case, at least in the modern Russian language. I wouldn't mind to be proven wrong though.
There is a discussion about the etymology of word запятая at gramota.ru.