Okay after hours of researching I came to the point that I should restart from draft. I simulate a Html form upload with following C# code:

  private async Task<string> UploadImage(StorageFile file)
        {
            HttpClient client = new HttpClient();
            client.BaseAddress = new Uri("http://your.url.com/");
            MultipartFormDataContent form = new MultipartFormDataContent();
            HttpContent content = new StringContent("fileToUpload");
            form.Add(content, "fileToUpload");
            var stream = await file.OpenStreamForReadAsync();
            content = new StreamContent(stream);
            content.Headers.ContentDisposition = new ContentDispositionHeaderValue("form-data")
            {
                Name = "fileToUpload",
                FileName = file.Name
            };
            form.Add(content);
            var response = await client.PostAsync("upload.php", form);
            return response.Content.ReadAsStringAsync().Result;
        }

And my php file to receive the data looks as the follwing:

<?php 
$uploaddir = 'uploads/';
$uploadfile = $uploaddir . basename($_FILES['fileToUpload']['name']);
echo '<pre>';
if (move_uploaded_file($_FILES['fileToUpload']['tmp_name'], $uploadfile)) {
    echo "File is valid, and was successfully uploaded.\n";
} else {
    echo "Possible file upload attack!\n";
}

echo 'Here is some more debugging info:';
print_r($_FILES);
?>

Now it works as it should and I hope somebody can reuse my code.