Thumb and Index Finger hurt while trying to play with palm muting

As I mentioned in the title, when i palm mute and try to pluck strings, my thumb and index finger ache. That also happens with my thumb when i just try to apply pressure on it, it has also got something like a little callus on it, my index finger however doesn't, but when applied pressure to it, it might ache aswell. Is there a way to prevent this from happening or do i just need to keep playing and get used to it?

 

Thanks!
However i want to use my palm to mute the strings because that forces me to play with the thumb and fingers and i want to get the thumb involved in my technique too, i don't want to put sponges and stuff to mute. Does string gauge affect this issue too? Maybe if i get lighter strings the pain will be reduced? Also, would flatwounds or tapewounds hurt less than roundwounds? Btw the pain i have is quite similar to what the beginners feel in their fingers when they first start playing the bass. Their fingers ache a bit, but then they get used to it and their fingers get stronger. Maybe that's whats happening to my thumb and index finger right now, even tho i've been playing bass for about a year and more

 

Thanks for your reply, but i don't want to use a pick. I tried it out, and i prefer the way of playing with the thumb and index. If i were to change the height of the bass then the part that aches wouldn't ache anymore, but i would begin to ache again. I think i just need to stop palm muting until those aching parts calm down, then i'll get back to it.
Note: The aching parts look like bubbles or something like that.

 

Yup, in the DIP joint area i got sth like a blister bubble. One on the thumb and one on the index.

 

thanks for your suggestion, i will do that!