Hi ahmadsubuhanl...,
You need to set the dropdownParent property to the id of the Panel control.
Refer below code.
HTML
<html xmlns="http://www.w3.org/1999/xhtml">
<head id="Head1" runat="server">
    <title></title>
    <style type="text/css">
        body { font-family: Arial; font-size: 10pt; }
        .modalBackground { background-color: Black; filter: alpha(opacity=40); opacity: 0.4; }
        .modalPopup { background-color: #FFFFFF; width: 460px; border: 3px solid #0DA9D0; }
        .modalPopup .header { background-color: #2FBDF1; height: 30px; color: White; line-height: 30px; text-align: center; font-weight: bold; }
        .modalPopup .body { min-height: 50px; line-height: 30px; text-align: center; padding: 5px; }
        .modalPopup .footer { padding: 3px; }
        .modalPopup .button { height: 23px; color: White; line-height: 23px; text-align: center; font-weight: bold; cursor: pointer; background-color: #9F9F9F; border: 1px solid #5C5C5C; }
        .modalPopup td { text-align: left; }
        .form-control { width: 200px !important; }
        .select2-selection__rendered { font-size: small !important; }
        .select2-results__option { font-size: large !important; }
    </style>
    <script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/jquery/1.9.1/jquery.min.js"></script>
    <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/select2/4.0.3/css/select2.min.css" />
    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/select2/4.0.3/js/select2.min.js"></script>
    <script type="text/javascript">
        $(function () {
            $(".js-example-placeholder-single").select2({
                placeholder: "Select",
                allowClear: true,
                dropdownParent: $('#pnlPopup'),
                width: 200
            });
        });
    </script>
</head>
<body>
    <form id="form1" runat="server">
    <asp:ScriptManager ID="ScriptManager1" runat="server">
    </asp:ScriptManager>
    <asp:LinkButton Text="" ID="lnkFake" runat="server" />
    <cc1:ModalPopupExtender ID="mpe" runat="server" PopupControlID="pnlPopup" TargetControlID="lnkFake"
        CancelControlID="btnClose" BackgroundCssClass="modalBackground">
    </cc1:ModalPopupExtender>
    <asp:Panel ID="pnlPopup" runat="server" CssClass="modalPopup" align="center" Style="display: none">
        <div class="header">
            New Loan
        </div>
        <div class="body">
            <table border="0" width="450" cellpadding="0" cellspacing="0">
                <tr>
                    <td>
                        <asp:Label ID="Label7" runat="server" Font-Names="Calibri" Font-Size="Smaller" Style="text-align: right"
                            Text="Jenis Pinjaman:"></asp:Label>
                    </td>
                    <td width="10">
                         
                    </td>
                    <td style="text-align: left">
                        <asp:DropDownList ID="ddlCustomers" runat="server" CssClass="js-example-placeholder-single">
                            <asp:ListItem Text="--Select Customer--" Value="0" />
                            <asp:ListItem Text="John Hammond" Value="1" />
                            <asp:ListItem Text="Mudassar Khan" Value="2" />
                            <asp:ListItem Text="Suzanne Mathews" Value="3" />
                            <asp:ListItem Text="Robert Schidner" Value="4" />
                        </asp:DropDownList>
                    </td>
                </tr>
            </table>
        </div>
        <div class="footer" align="right">
            <asp:Button ID="btnClose" runat="server" CssClass="button button3" Text="Close" ToolTip="Close" />
            <asp:Button ID="Button3" runat="server" Text="Save" ToolTip="Save" CssClass="button button2" />
        </div>
    </asp:Panel>
    </form>
</body>
</html>
Code
C#
protected void Page_Load(object sender, EventArgs e)
{
    mpe.Show();
}
VB.Net
Protected Sub Page_Load(ByVal sender As Object, ByVal e As EventArgs) Handles Me.Load
    mpe.Show()
End Sub
Screenshot
