I guess that this is one of those examples where translation becomes really hard and, in a way, a bit ambiguous either way. At this point I would rather see the general meaning in Japanese and associate it to whatever the closest image that I can get in my mind, rather than thinking of a specific word.
However, when we have to translate, we need words and choosing the most accurate ones might be as tricky as interesting.
To get to your question, what does actually "account" even mean in English? Let's look it up on a dictionary. Obviously at first we all think about the "physical account", with the standard meaning of:
a. A formal banking, brokerage, or business relationship established to provide for regular services, dealings, and other financial transactions.
However, if we keep reading we find out that actually account also means:
c. A sum of money deposited for checking, savings, or brokerage use.
(The above examples are taken from here: http://www.thefreedictionary.com/account)
Therefore, if you think that in English as well the word account has the meaning given above I would say that the answer is yes, it can actually mean account (since also in English account might refer to the money, like the definition you give in Japanese).
In the end I guess that the confusion can mostly rise from the fact that in English as well account has different meanings although we usually think of one (example a.).
By the way, another example to add to your question is 普通預金{ふつうよきん} that can be translated as "ordinary account".
I think that also reading the wiki page for 預金 might give more insight:
https://ja.wikipedia.org/wiki/%E9%A0%90%E9%87%91
Edit: to add more to it, I think it's interesting here to look at the kanji 預 by itself. This has the meaning of deposit, custody, entrust to etc (think it as the verb 預ける for example). So you can think of 預金 as a sum of money that is being entrusted/deposited to someone/somewhere. The exact same definition of "account" in English that I reported above in case you're putting it in a bank...account. :)