I can't think of a way to do it with a single s///, but this works:

use strict;
use warnings;

my $str = "abcdefghiaabccdjklm";
my @chars = split //, $str;
my %uniq;
$uniq{$_}++ for @chars;
$str = '';
for (@chars) {
    $str .= $_ unless $uniq{$_} > 1;
}
print $str;

__END__

efghijklm
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