stoma is Greek for mouth.
–stomia is stoma plus an abstract noun ending: “-mouth-ation”.
In medicine, a Stoma (medicine) is also a surgically made opening. So a colostomy is a surgical intervention creating an opening (a stoma, a “mouth”) in the colon: kōlo-stom-ia > colostomy, “colon-mouth-ation”. The Wikipedia article gives 16 other stoma operations.
The -o- is not part of any suffix: it’s how Greek connects words together in a compound.