diff --git a/lib/matplotlib/backend_bases.py b/lib/matplotlib/backend_bases.py
index 37d7d276ea93..7a434d5b22ad 100644
--- a/lib/matplotlib/backend_bases.py
+++ b/lib/matplotlib/backend_bases.py
@@ -3245,6 +3245,11 @@ def _update_view(self):
             ax._set_position(pos_active, 'active')
         self.canvas.draw_idle()
 
+    def configure_subplots(self, *args):
+        from matplotlib import pyplot as plt
+        tool = plt.subplot_tool(self.canvas.figure)
+        tool.figure.canvas.manager.show()
+
     def save_figure(self, *args):
         """Save the current figure."""
         raise NotImplementedError
diff --git a/lib/matplotlib/backends/_backend_tk.py b/lib/matplotlib/backends/_backend_tk.py
index bc31d31e699b..3209d7db7ae4 100644
--- a/lib/matplotlib/backends/_backend_tk.py
+++ b/lib/matplotlib/backends/_backend_tk.py
@@ -583,16 +583,6 @@ def _Spacer(self):
         s.pack(side=tk.LEFT, padx=5)
         return s
 
-    def configure_subplots(self):
-        toolfig = Figure(figsize=(6, 3))
-        window = tk.Toplevel()
-        canvas = type(self.canvas)(toolfig, master=window)
-        toolfig.subplots_adjust(top=0.9)
-        canvas.tool = SubplotTool(self.canvas.figure, toolfig)
-        canvas.draw()
-        canvas.get_tk_widget().pack(side=tk.TOP, fill=tk.BOTH, expand=1)
-        window.grab_set()
-
     def save_figure(self, *args):
         filetypes = self.canvas.get_supported_filetypes().copy()
         default_filetype = self.canvas.get_default_filetype()
diff --git a/lib/matplotlib/backends/backend_gtk3.py b/lib/matplotlib/backends/backend_gtk3.py
index 62eb324ebce1..a1a1c6544e25 100644
--- a/lib/matplotlib/backends/backend_gtk3.py
+++ b/lib/matplotlib/backends/backend_gtk3.py
@@ -587,34 +587,6 @@ def on_notify_filter(*args):
         except Exception as e:
             error_msg_gtk(str(e), parent=self)
 
-    def configure_subplots(self, button):
-        toolfig = Figure(figsize=(6, 3))
-        canvas = type(self.canvas)(toolfig)
-        toolfig.subplots_adjust(top=0.9)
-        # Need to keep a reference to the tool.
-        _tool = SubplotTool(self.canvas.figure, toolfig)
-
-        w = int(toolfig.bbox.width)
-        h = int(toolfig.bbox.height)
-
-        window = Gtk.Window()
-        try:
-            window.set_icon_from_file(window_icon)
-        except Exception:
-            # we presumably already logged a message on the
-            # failure of the main plot, don't keep reporting
-            pass
-        window.set_title("Subplot Configuration Tool")
-        window.set_default_size(w, h)
-        vbox = Gtk.Box()
-        vbox.set_property("orientation", Gtk.Orientation.VERTICAL)
-        window.add(vbox)
-        vbox.show()
-
-        canvas.show()
-        vbox.pack_start(canvas, True, True, 0)
-        window.show()
-
     def set_history_buttons(self):
         can_backward = self._nav_stack._pos > 0
         can_forward = self._nav_stack._pos < len(self._nav_stack._elements) - 1
diff --git a/lib/matplotlib/backends/backend_wx.py b/lib/matplotlib/backends/backend_wx.py
index f1887a886576..099ae5e6fe11 100644
--- a/lib/matplotlib/backends/backend_wx.py
+++ b/lib/matplotlib/backends/backend_wx.py
@@ -1186,26 +1186,6 @@ def pan(self, *args):
         self.ToggleTool(self.wx_ids['Zoom'], False)
         NavigationToolbar2.pan(self, *args)
 
-    def configure_subplots(self, *args):
-        global FigureManager  # placates pyflakes: created by @_Backend.export
-        frame = wx.Frame(None, -1, "Configure subplots")
-        _set_frame_icon(frame)
-
-        toolfig = Figure((6, 3))
-        canvas = type(self.canvas)(frame, -1, toolfig)
-
-        # Create a figure manager to manage things
-        FigureManager(canvas, 1, frame)
-
-        # Now put all into a sizer
-        sizer = wx.BoxSizer(wx.VERTICAL)
-        # This way of adding to sizer allows resizing
-        sizer.Add(canvas, 1, wx.LEFT | wx.TOP | wx.GROW)
-        frame.SetSizer(sizer)
-        frame.Fit()
-        SubplotTool(self.canvas.figure, toolfig)
-        frame.Show()
-
     def save_figure(self, *args):
         # Fetch the required filename and file type.
         filetypes, exts, filter_index = self.canvas._get_imagesave_wildcards()
diff --git a/lib/matplotlib/pyplot.py b/lib/matplotlib/pyplot.py
index 1314f055ec5d..3e9088073cb9 100644
--- a/lib/matplotlib/pyplot.py
+++ b/lib/matplotlib/pyplot.py
@@ -1453,19 +1453,19 @@ def subplot_tool(targetfig=None):
     """
     Launch a subplot tool window for a figure.
 
-    A :class:`matplotlib.widgets.SubplotTool` instance is returned.
+    A `matplotlib.widgets.SubplotTool` instance is returned.
     """
     if targetfig is None:
         targetfig = gcf()
-
-    with rc_context({'toolbar': 'None'}):  # No nav toolbar for the toolfig.
-        toolfig = figure(figsize=(6, 3))
-    toolfig.subplots_adjust(top=0.9)
-
-    if hasattr(targetfig.canvas, "manager"):  # Restore the current figure.
-        _pylab_helpers.Gcf.set_active(targetfig.canvas.manager)
-
-    return SubplotTool(targetfig, toolfig)
+    with rc_context({"toolbar": "none"}):  # No navbar for the toolfig.
+        # Use new_figure_manager() instead of figure() so that the figure
+        # doesn't get registered with pyplot.
+        manager = new_figure_manager(-1, (6, 3))
+    manager.set_window_title("Subplot configuration tool")
+    tool_fig = manager.canvas.figure
+    tool_fig.subplots_adjust(top=0.9)
+    manager.show()
+    return SubplotTool(targetfig, tool_fig)
 
 
 # After deprecation elapses, this can be autogenerated by boilerplate.py.
diff --git a/lib/matplotlib/widgets.py b/lib/matplotlib/widgets.py
index ba0168e48a17..8c95ebd38179 100644
--- a/lib/matplotlib/widgets.py
+++ b/lib/matplotlib/widgets.py
@@ -1099,6 +1099,7 @@ def __init__(self, targetfig, toolfig):
             The figure instance to embed the subplot tool into.
         """
 
+        self.figure = toolfig
         self.targetfig = targetfig
         toolfig.subplots_adjust(left=0.2, right=0.9)
         toolfig.suptitle("Click on slider to adjust subplot param")