No, jpa doesn't provide any feature to define or create indexes. For some (unknown to me) reason, it's only possible to create unique indexes in JPA.
If you are not using hibernate or if you really don't want to use those annotations, you'll need to build your annotations and processor to output or update the database accordingly, but I don't think it's very trivial (and it's definitely, non standard)
Edit
Here's an example of how to define an index with Hibernate
@org.hibernate.annotations.Table(
appliesTo = "table_name",
indexes = {
@Index(name="single_column_index", columnNames = "col"),
@Index(name="multi_column_index", columnNames = {"col1", "col2"}),
}
)