You're already using Exporter.

Exporter is capable of exporting variables as well as subs.

Is there a reason you aren't just exporting your $var, which would make it a member of both namespaces?

In prog.pl:

#!/usr/bin/env perl

use strict;
use warnings;
use 5.010;

use lib '.';
use MyModule;

my_sub;

say "Main program: $var";
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In MyModule.pm:

package MyModule;

use strict;
use warnings;
use 5.010;

use base 'Exporter';

our $var;

our @EXPORT = qw( my_sub $var );

sub my_sub {
  $var = 42;

  say "Set \$var to $var in my_sub";
}
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Result:

$ ./prog.pl 
Set $var to 42 in my_sub
Main program: 42
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