I know this is an old question, but gracchus's solution doesn't work if file names contain spaces. VonC's solution to file names with spaces is to not remove them utilizing --ignore-unmatch, then remove them manually, but this will not work well if there are a lot.
Here is a solution that utilizes bash arrays to capture all files.
# Build bash array of the file names
while read -r file; do
rmlist+=( "$file" )
done < <(git ls-files -i --exclude-standard)
git rm –-cached "${rmlist[@]}"
git commit -m 'ignore update'