IPC::Open3 or IPC::Run provide facilities for running external programs and capturing standard error separately from standard output, but be warned, it's easy to deadlock.

However you may find that using Net::LDAP better suits your needs. Since the attempted LDAP updates occur within your program checking the result is fairly easy.

use Net::LDAP;

my $ldap = Net::LDAP->new( ... );
my $mesg = $ldap->modify( ... );
if ( $mesg->is_error() ) {
    ...
}
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