I don't see that at all.

$host = '127.0.0.1';
my $output = `ping $host`;
print "ping result $output\n";
[download]

outputs

ping result
Pinging 127.0.0.1 with 32 bytes of data:

Reply from 127.0.0.1: bytes=32 time<10ms TTL=128
Reply from 127.0.0.1: bytes=32 time<10ms TTL=128
Reply from 127.0.0.1: bytes=32 time<10ms TTL=128
Reply from 127.0.0.1: bytes=32 time<10ms TTL=128

Ping statistics for 127.0.0.1:
    Packets: Sent = 4, Received = 4, Lost = 0 (0% loss),
Approximate round trip times in milli-seconds:
    Minimum = 0ms, Maximum =  0ms, Average =  0ms
[download]

Is that what you get from that three line program?

I tried fooling with binmode, $/ and $\ to reproduce your undesirable results to no avail. Are you using cygwin or ActiveState?

Have you tried using a module like Net::Ping instead?