Import PEM into Java Key Store

First, convert your certificate in a DER format :

openssl x509 -outform der -in certificate.pem -out certificate.der

And after, import it in the keystore :

keytool -import -alias your-alias -keystore cacerts -file certificate.der

If you only want to import a certificate in PEM format into a keystore, keytool will do the job:

keytool -import -alias *alias* -keystore cacerts -file *cert.pem*