1)Backup Certificates.
sudo cp /System/Library/Keychains/SystemRootCertificates.keychain /System/Library/Keychains/SystemRootCertificates.keychain.bak
2)Extract "SHA1" from the specific Certificate.
3)Delete Certificate.
sudo security delete-certificate -Z "SHA1" /System/Library/Keychains/SystemRootCertificates.keychain