Don’t see them as through hole anywhere, but the pico blade smds may do you. In the search bar in the parts bin enter pico blade and the series will come up. If they won’t do you will need a custom part.
edit: It is your lucky day. I happened to need an example of a sub .1in pitch part and these at 1.25mm pitch fill the bill nicely, so we both get what we want:
Micro JST 2 pin.fzpz (7.7 KB)
Micro JST 2 pin-altbb.fzpz (7.1 KB)
Micro JST 3 pin.fzpz (8.4 KB)
Micro JST 3 pin altbb.fzpz (7.3 KB)
There are 4 rather than 2 because I needed alternate breadboards, one with an SMD adapter plate with connectors on .1in pitch (even though these aren’t SMD) and one with the just the connector on 1.25mm centers. They are otherwise identical, so use whichever suits. The holes in pcb are 0.020in, the pin is shown as 0.035mm (0.00138in) however given the source the hole may not be the correct size. I would advise ordering the smallest/ least number of boards you can with just a connector on it to verify the hole size before committing to a more complex board (or find a 0.02in drill and see if it will fit the part). The pad is oblong to give at least some room to solder (the width is the recommended SMD width).