I think you can try specify it in OptionSettings of AWS::ElasticBeanstalk::Application. You could try something like that:
{
"Namespace": "aws:elb:loadbalancer",
"OptionName": "LoadBalancerHTTPSPort",
"Value": "443"
}
{
"Namespace": "aws:elb:loadbalancer",
"OptionName": "SSLCertificateId",
"Value": "Your certificate ARN"
}
I didn't test it, so it is no guarantee that it will work.