You need to call destroy on the target widget. When you create the button, do something like this:

$win->Button(-text => 'OK', -command => [\&ok, $win])->pack;
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This will call ok($win) whenever the OK button is triggered (In general, \&ok is clearer than sub { ok() }). ok() then becomes:

sub ok
{
  my $win = shift;
  $win->destroy;
  $notified = 1;
}
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