Yes and no.
Yes: X.509 certificates almost always have either a keyUsage or a extendedKeyUsage extension, which regulates how the certificate is to be used. If you ommit the values dataEncipherment and keyEncipherment at this point and set it to something else (like digitalSignature) , every application adhering to the standard must not use the certificate's key for encryption.
No: Every X.509 certificate contains a public key which can theoretically be used to encrypt data, no matter what the standard orders you to do.
Bottom line: You can not technically prohibit someone from doing encryption with a key in a X.509 certificate. Your best shot is to set the keyUsage to a appropriate value and to use an ECC key instead of an RSA key, since ECC encryption is something that is not done very often.