pipe each line of a file to a command

You can use Python for that (no need for reading each line):

python -m base64 -d foo.txt

This works for me in base64 8.13:

base64 --decode test.txt

No need to split the file. Which version are you using?

Use base64 --decode together with a loop:

$ while IFS= read -r line; do echo "$line" | base64 --decode; done < file
cat
dog
house