Using dropdownZIndex as opts. Dropping default value so use can set it via css.

select2.js

@@ -539,7 +539,6 @@
                 formatInputTooShort: function (input, min) { return "Please enter " + (min - input.length) + " more characters"; },
                 minimumResultsForSearch: 0,
                 minimumInputLength: 0,
-                zIndex: 2000,
                 id: function (e) { return e.id; },
                 matcher: function(term, text) {
                     return text.toUpperCase().indexOf(term.toUpperCase()) >= 0;
@@ -650,13 +649,15 @@
             var offset = this.container.offset();
             var height = this.container.outerHeight();
             var width  = this.container.outerWidth();
-
-            this.dropdown.css({
+            var css    = {
                 top: offset.top + height,
                 left: offset.left,
-                width: width,
-                "z-index": this.opts.zIndex
-            });
+                width: width
+            }
+            if (this.opts.dropdownZIndex !== undefined) {
+                css["z-index"] = this.opts.dropdownZIndex
+            }
+            this.dropdown.css(css);
         },
 
         open: function () {