Etymolonline states that the word "suffix" is of Latin Origin. However, the Hebrew word for "end" is sof (סוף) pronounced like in "sofa".
Since a suffix comes at the end of the word, I often thought that it may be the actual origin.
Or is it just a coincidence?
It is pure coincidence, I’m afraid.
‘Suffix’ is a Latin word, and it can be split up into sub- ‘under, after’ and fixus, the passive perfect participle of figō ‘fix, fasten, stick to, bore through’. Literally, it just means ‘[something] stuck to the bottom/end (of …)’. Similarly, ‘prefix’ means ‘[something] stuck to the beginning (of …)’, ‘infix’ means ‘[something] stuck inside (of …)’, ‘affix’ means ‘[something] stuck to (…)’, and ‘circumfix’ means ‘[something] stuck around (…)’.
Even a connection between Latin sub- and Hebrew sof is not likely, because Latin sub- is quite simply the non-transparent result of an earlier compound preposition exupo- ‘out from under’ (made up of ex- ‘from’ and upo- ‘under’) in very early pre-Italic. The preposition upo was lost as a standalone preposition and prefix very early on in Italic languages, but exupo survived and took its place. By aphaeresis, regular syncope, and semi-regular prefix lenition, *exupo- became *’ksupo- > *’supo- (aphaeresis), then *sup- (syncope), and finally *sub- (prefix lenition).
So in the case of ‘suffix’ specifically, the f comes from the verb meaning ‘fasten’ and is not connected to the prefix sub-; while in the case of sub- itself, the s comes from a different word than the ub.
Unless Hebrew sof ‘end’ happens to be a borrowing from an Italic language (which I think would be quite odd, considering that sub- only occasionally means ‘after’, its basic meaning being ‘under’—I do not know the etymology of sof, however), there really is no way that the two words can be related.
I gotta say, given affix, prefix, and infix, it would be a huge coincidence if they all came from Latin but suffix were Hebrew.
It might be that there's a PIE root for "end" or "under" that sounded like "su-".
Latin and English are members of a completely different family of languages (Indogermanic/Indoeuropean) than Hebrew (Semitic). Suffix has nothing to do with Hebrew, Janus explained it correctly. Imperium also has nothing to do with Hebrew. It is Latin and derives from impero, -as, -are which means "to order or to command" and which itself consists of im- ("in") + parare ("to prepare or to order"). "Syfer" in Afrikaans (also Indogerm./Indoeurop.) or "Ziffer" in German are loanwords (via Italian) from Arabic "sifr" which itself seems to be a loanword or adaptation from Middle Greek or Old Indic, but I'd have to look that up.
I would not discount the possibility suggested by the OP, seeing that Ancient/Classical/Biblical Hebrew is much older than Latin. In view of many more of these 'coincidences' all over English, I would advance that Latin-based languages has borrowed greatly from Hebrew especially when it comes to prefixes and suffixes.
Like the ad (He: towards) in ad hoc and ad infinitum. This is also present in English words like advent.
The em/im prefix of empire (La: imperium [with[along]-perimeter]) where the Hebrew has the self standing word im (He: with) also seen in the beautiful title of the Lord Jesus, Em-[m]anu-el (with-us-God). This is also seen in words like empathy.
The short sounding o (He: or) is or in English.
Adereth (He:glory/cloak) to English adore along with Adi-ir (He:majestic).
And I can think of one more in Afrikaans: soferah (He: counting) -> syfer (numbers used for counting).
And of course the a ending in feminine names like America, Brittanica, Russia might even have a relation to the general feminine ending of -a in Hebrew.
Edit
Even today there are two ways to pronounce b and v/w (v in certain pronunciations not that far from f) sounds in Hebrew. The Ashkenazi and Sephardic ways, so I honestly think there is a fair argument for a connection to Hebrew through Latin. Noting that languages develop primarily by sound (euphonics) and then by spelling.
