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?
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.
Word запятая is derived from verb запинаться as
(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.