EF6 code first relationship between entities

You could try with the following, code:

[Table("Fracao")]
    public class Fracao
    {


        [ScaffoldColumn(false)]
        public int FracaoID { get; set; }

        public int? ProprietarioID { get; set; }

        [InverseProperty("ID")]
        [ForeignKey("ProprietarioID")]
        public virtual Proprietario Proprietario { get; set; }

        [Required]
        public int CondominioID { get; set; }
        public virtual Condominio Condominio { get; set; }

        [Required]
        public int ZonaID { get; set; }
        public virtual Zona Zona { get; set; }

        [Required, StringLength(4), Display(Name = "Letra")]
        public string Letra { get; set; }

        [Required, Display(Name = "Área")]
        public decimal Area { get; set; }

        [Required, Display(Name = "Permilagem")]
        public decimal Permilagem { get; set; }

        [Required, StringLength(4), Display(Name = "Piso")]
        public string Piso { get; set; }

        [Required, StringLength(10), Display(Name = "Porta")]
        public string Porta { get; set; }

    }

Because with [ForeignKey("ProprietarioID")], you tell the annotation that FK is the one defined within it.

Update

Errata, I did not pay attention to the fact that your identifier has the same name as the foreign key, so please remove the annotation [InverseProperty("ID")].

Update 2

With the following code, which I replicated entirely on my machine, worked perfectly, try to do the same, as a test, as a new project:

DbContext class:

public class TesteContext : DbContext
{
    public DbSet<Fracao> Fracoes { get; set; }
    public DbSet<Proprietario> Proprietarios { get; set; }
}

Fraction Class:

[Table("Fracao")]
public class Fracao
{
    [ScaffoldColumn(false)]
    public int FracaoID { get; set; }

    public int? ProprietarioID { get; set; }

    [ForeignKey("ProprietarioID")]
    public virtual Proprietario Proprietario { get; set; }

    [StringLength(4), Display(Name = "Letra")]
    public string Letra { get; set; }

    [Display(Name = "Área")]
    public decimal Area { get; set; }

    [Display(Name = "Permilagem")]
    public decimal Permilagem { get; set; }

    [StringLength(4), Display(Name = "Piso")]
    public string Piso { get; set; }

    [StringLength(10), Display(Name = "Porta")]
    public string Porta { get; set; }

}

Owner Class:

[Table("Proprietario")]
public class Proprietario
{
    [ScaffoldColumn(false)]
    public int ProprietarioID { get; set; }

    [StringLength(255), Display(Name = "Nome")]
    public string Nome { get; set; }

    [StringLength(500), Display(Name = "Morada"), DataType(DataType.MultilineText)]
    public string Morada { get; set; }

    [StringLength(30), Display(Name = "CPostal")]
    public string CPostal { get; set; }

    [StringLength(100), Display(Name = "Localidade")]
    public string Localidade { get; set; }

    [StringLength(10), Display(Name = "Telefone")]
    public string Telefone { get; set; }

    [StringLength(10), Display(Name = "Telemovel")]
    public string Telemovel { get; set; }

    [DataType(DataType.EmailAddress), Display(Name = "Email")]
    public string Email { get; set; }

    [StringLength(10), Display(Name = "Contribuinte")]
    public string Contribuinte { get; set; }

    public virtual ICollection<Fracao> Fracoes { get; set; }
}

And the codes of a console program:

using (var db = new TesteContext())
{
    // Create and save a new Blog 
    Console.Write("Enter a name for a new Blog: ");
    var name = Console.ReadLine();

    var proprietario = new Proprietario { Email = "oi" };
    proprietario = db.Proprietarios.Add(proprietario);
    db.SaveChanges();

    var fracao = new Fracao { Area = 1, Proprietario = proprietario };
    db.Fracoes.Add(fracao);
    db.SaveChanges();

    // Display all Blogs from the database 
    var query = from b in db.Fracoes
                orderby b.Area
                select b;

    Console.WriteLine("All blogs in the database:");
    foreach (var item in query)
    {
         Console.WriteLine(item.Area);
    }

    Console.WriteLine("Press any key to exit...");
    Console.ReadKey();
}

With this code, you can enter a fraction and an owner, doing the binding correctly, if you want to do the update, you will have to do the following:

var fracao = new Fracao { Area = 1, Proprietario = null, ProprietarioId = proprietario.ProprietarioId };

Try again with these codes and comment if you achieve.