Parsing substrings from a command

Try this (Shellcheck-clean) pure Bash code:

#! /bin/bash

# Regular expressions to match the required fields
name_rx='^Certificate[[:space:]]+Name:[[:space:]]+(.*)$'
domains_rx='^Domains:[[:space:]]+(.*)$'

certbot_auto_output=$(certbot-auto certificates)

# (Assuming a standard $IFS) 'read' will strip leading and trailing whitespace
while read -r line ; do
    if [[ $line =~ $name_rx ]] ; then
        certificate=${BASH_REMATCH[1]}
    elif [[ $line =~ $domains_rx ]] ; then
        domains=${BASH_REMATCH[1]}
        domains=${domains// /,}     # Replace spaces with commas
        printf 'certificate="%s"\n' "$certificate"
        printf 'domains="%s"\n' "$domains"
    fi
done <<<"$certbot_auto_output"

See mkelement0's excellent answer to How do I use a regex in a shell script? for information about using Bash regular expressions.

See Substituting part of a string (BashFAQ/100 (How do I do string manipulation in bash?)) for information about ${var//.../...}.

See Command line: <<< instead of << for information about <<<"..." ("here string").

Used funkyjelly's response to come up with the following:

# Store each certificate name and list of domains in an array
mapfile -t certificate_names < <(/opt/certbot-auto certificates | grep 'Certificate Name:' | cut -d':' -f2) 
mapfile -t domains < <(/opt/certbot-auto certificates | grep 'Domains:' | cut -d':' -f2) 

len=${#certificate_names[@]}

for (( i=0; i<$len; i++ ))
do
    #replace spaces with commas and drop the first comma
    fqdns=${domains[$i]}
    fqdns=${fqdns// /,}
    fqdns="${fqdns:1}"

    # Renew the cert
    /opt/certbot-auto certonly --manual --agree-tos --manual-public-ip-logging-ok --email [email protected] --preferred-challenges dns --manual-auth-hook update-txt-records.sh --manual-cleanup-hook clean-txt-records.sh --cert-name ${certificate_names[$i]} -d $fqdns --expand --noninteractive

done