If you used a self-signed certificate, this would have been created within a keystore. Be sure the new keystore is properly defined in the [install-dir]/conf/VHosts.xml file.
When you follow the instructions for generating and importing a certificate, this will create a new keystore that should be used with your VHosts.xml configuration.
The Java keystore will require a private key certificate (generated in the keystore with the CSR generation steps), a signed certificate returned from the CA with your CSR submission and intermediary certificates or CA bundles.
You may find the steps in the SSL troubleshooting article helpful, when verifying these certificates have been imported properly.