An older use of the word "prove", as in to test, means it says "that's an exception that tests the rule, and finds it is incorrect"
So the (existence of an) exception proves (the existence of) the rule.
L'exception qui confirme la règle
And there's no ambiguity about it, the exception is confirming that the rule is true.
That's a stupid expression IMO, but I would be surprised if the English expression meant the exact contrary.
Hmmm... self-referential vibes coming here. It might be that the only exception to the R1 is itself, but then... etc.
I wouldn't use the phrase outside of silly internet jokes about 90s popcorn flicks.
If your rule is that carpenters are usually men and someone goes into a carpentry conference with 1000 carpenters and points out that 50 of them are women, you get to say "exception that proves the rule" and be right.
If your rule is that carpenters are usually women and someone goes into a carpentry conference with 1000 carpenters and points out that 950 of them are men, that's not the exception that proves the rule because 95% of the target population doesn't qualify as an exception.