How do I delete a system file from Time Machine?

After consulting this support document, I tried to delete a Safari cache file that was captured by Sophos's Quarantine Manager as containing a common phishing hook. But it's in Library and Time Machine can't locate it. The Library folder, as you know, is typically hidden, and it wasn't there when I went to the starfield.
It's not a big threat to me, and will soon disappear from my cache, but it bugs me that I can't get to it.

Enter Time Machine from within your user Library folder. That will bring you to your user Library within Time Machine. (Your user Library is visible under the Go menu in Finder if you hold down the Option key.)

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