Web app and web api authentication in same application

I have a web app MVC,using auth0 owin regular web app cookie based authentication.

This web app also has webapis which is used internally in the application. However i have a requirement to call this webapis from outside the application. So i created a restclient and tried to implement jwtbearerauthentication in application (but cookie based on authentication still in place).

Now when i call the webapi from other application it validates the bearer token gives no error however it redirects to login page due to cookie based authentication.

startup file:

 public partial class Startup
{
    private IPlatform platform;
    public void ConfigureAuth(IAppBuilder app, IPlatform p, IContainer container)
    {
        platform = p;


        // Enable the application to use a cookie to store information for the signed in user
        app.UseCookieAuthentication(new CookieAuthenticationOptions
        {
            AuthenticationType = DefaultAuthenticationTypes.ApplicationCookie,
            LoginPath = new PathString("/Account/Login"),
            ExpireTimeSpan = System.TimeSpan.FromDays(2),
            SlidingExpiration = true
        });

        // Use a cookie to temporarily store information about a user logging in with a third party login provider
        app.UseExternalSignInCookie(DefaultAuthenticationTypes.ExternalCookie);
        var provider = new Auth0.Owin.Auth0AuthenticationProvider
        {
            OnReturnEndpoint = (context) =>
            {
                // xsrf validation
                if (context.Request.Query["state"] != null && context.Request.Query["state"].Contains("xsrf="))
                {
                    var state = HttpUtility.ParseQueryString(context.Request.Query["state"]);
                    AntiForgery.Validate(context.Request.Cookies["__RequestVerificationToken"], state["xsrf"]);
                }

                return System.Threading.Tasks.Task.FromResult(0);
            },
            OnAuthenticated = (context) =>
            {
                var identity = context.Identity;
                //Add claims
                var authenticationManager = container.Resolve<IAuthenticationManager>();
                authenticationManager.AddClaims(identity);

                if (context.Request.Query["state"] != null)
                {
                    authenticationManager.AddReturnUrlInClaims(identity, context.Request.Query["state"]);
                }

                return System.Threading.Tasks.Task.FromResult(0);
            }
        };

        var issuer = "https://" + ConfigurationManager.AppSettings["auth0:Domain"] + "/";
        var audience = ConfigurationManager.AppSettings["auth0:ClientId"];
        var secret = TextEncodings.Base64.Encode(TextEncodings.Base64Url.Decode(ConfigurationManager.AppSettings["auth0:ClientSecret"]));
        app.UseJwtBearerAuthentication(
            new JwtBearerAuthenticationOptions
            {
                AuthenticationMode = Microsoft.Owin.Security.AuthenticationMode.Active,
                AllowedAudiences = new[] { audience },
                IssuerSecurityTokenProviders = new IIssuerSecurityTokenProvider[]
                {
                    new SymmetricKeyIssuerSecurityTokenProvider(issuer, secret)
                }
            });

        app.UseAuth0Authentication(
            clientId: platform.ServerRole.GetConfigurationSettingValue("auth0:ClientId"),
            clientSecret: platform.ServerRole.GetConfigurationSettingValue("auth0:ClientSecret"),
            domain: platform.ServerRole.GetConfigurationSettingValue("auth0:Domain"),
            provider: provider);
    }
}

webapiconfig file:

     public static void Register(HttpConfiguration config)
    {

        // Web API routes
        config.MapHttpAttributeRoutes();
        config.Routes.MapHttpRoute("DefaultApi", "api/{controller}/{id}", new {id = RouteParameter.Optional});
        config.Filters.Add(new AuthorizeAttribute());
        ODataConfig.Setup(config);

        var clientID = WebConfigurationManager.AppSettings["auth0:ClientId"];
        var clientSecret = WebConfigurationManager.AppSettings["auth0:ClientSecret"];

        config.MessageHandlers.Add(new JsonWebTokenValidationHandler()
        {
            Audience = clientID,
            SymmetricKey = clientSecret
        });
    }

Currently creating the jwt token from below code and posting using postman in header just to check if it works.. but redirects to login page.

  string token = JWT.Encode(payload, secretKey, JwsAlgorithm.HS256);