The following code will work as you expected:

package Foo;
our $d;              #the only line added

sub top {
    my($fn) = @_;
    our($d) = ["a", "b"];
    printf "Top before %s [%s]\n", $d, join(",", @$d);
    $fn->($d);
    printf "Top After %s [%s]\n", $d, join(",", @$d);
}


package Bar;

Foo::top(sub {
    #our($d) = @_;  #removed!
    printf "  Before %s [%s]\n", $d, join(",", @$d);
    $d = [];
    printf "  After %s [%s]\n", $d, join(",", @$d);
});
[download]

The lexical scope is bordered by the innermost curly brackets or the boundaries of the file :) You must declare your variable in the lexical scope which includes all scopes where you want to see this variable. This is why i added the line our $d;

If you define the variable $d with our in the different packege, it is supposed to be a DIFFERENT $d variable. This is why i commented out the line in the second package.

See our() manpage for more details.

UPD: added execution result:

Top before ARRAY(0x1a60b7c) [a,b]
  Before ARRAY(0x1a60b7c) [a,b]
  After ARRAY(0x1a60bb8) []
Top After ARRAY(0x1a60bb8) []
[download]