Short answer: Technically, no, but your reasoning is not really false.
Two ways to see it:
1. Parfait can be considered the past participle of the verb "parfaire", which is neither a compound word in the French sense (two French words put together) nor in the English sense, as "par" is here technically a "préfixe", that is a particle commonly put behind the radical to form the word, like "parvenir", "parcourir", "parachever". It is, you guessed it correctly, a variant of per, meaning "through" in Latin.
2. Parfait, like its English counterpart perfect and other European words is in fact derived from the Latin "perfect passive participle" perfectus and is as such a single, non-compound word. Perfectus like its basic form perficio, is composed of per- (through) + facere (to do) meaning "to carry out".
However, although that basic form perficio is composed of multiple morphemes in Latin, it's still not a compound, but a derivation. Compounds are considered to be formed from two different independent lexemes, instead of an affix + an independent lexeme. While Latin did have a word per, what is present in perficio and many such words is the prefix per- (etymologically connected, of course).
I like to give these two similar explanations because they highlight the particularities of European Latin etymologies.