@ParaDice is right, but I thought I'd add a bit of a breakdown of the logic needed to arrive at that conclusion.
I'll break your passage up a bit
Her features were those of a woman about fifty, who had once been handsome.
The woman being described looks about 50 years old, it's clear that she was once good looking (implying that her looks have faded somewhat)
Sorrow and weeping had left traces upon them
Them here refers to a recent plural which has been marked. The lady's features fit the bill.
which not time itself would ever have produced without their aid;
Something has marked the features of her face. Time is the greatest enemy of youthful looks, but even time could not have done alone what has been done without help from something, again plural.
Sorrow and weeping fit here
There are rules of sentences which dictate which entity articles refer to, but if I'm honest, the above is how I, an English native, actually figure out what's going on in tortuous passages like the example. Hope this helps.