I would use IPC::Open3 for this. You can open two filehandles simultaneously, one for STDOUT and one for STDERR and collect their respective outputs into two separate scalars:

use strict;
use warnings;
use IPC::Open3;

my ($msg_out,$err_out);

eval { open3(undef, *OUT, *ERR, @ARGV) };

if ($@) {
    $msg_out = '';
    $err_out = "invalid command '$ARGV[0]'";
}
else {
    $msg_out = do {local $/;<OUT>};
    $err_out = do {local $/;<ERR>};
}

print "STDOUT: $msg_out\n";
print "STDERR: $err_out\n";
[download]

./foo.pl ls -la

./foo.pl some_command_that_does_not_exist

./foo.pl perl -le 'die "goodbye cruel world"'

UPDATE: Good point, Aristotle. This code indeed does not record STDOUT and STDERR as they occur, but is that really a reasonable request? Have you ever had need for such? I can't say that i have ... :-/

L-LL-L--L-LL-L--L-LL-L--
-R--R-RR-R--R-RR-R--R-RR
B--B--B--B--B--B--B--B--
H---H---H---H---H---H---
(the triplet paradiddle with high-hat)