1/r² is for an isotropic radiator, but Voyager 1 mounts (thankfully) a high gain directional antenna. The gains seem to be 36dBi or 48dBi, depending on the frequency [1]. This means that when pointed towards Earth, the signal power is actually between 4000 to 63000 times stronger than what that formula would give you. It's still tiny, but not as bad as that would suggest.
[1]: https://space.stackexchange.com/questions/65801/what-are-the...