It looks like you need to put the contents of "multiutil <cmd>" into a single string:

use warnings;
use strict;
use Sys::Hostname;
use Net::SMTP;

my $hostname = hostname;

my $Log_File = "E:/Backups/LOGs/Sync_Import.log";

open LOG, '>>', $Log_File or die "Cannot open '$Log_File' $!";
select LOG;  # Make LOG the default output filehandle

my $body0 = 'This message sent by the Import Process';
my $body1 = `multiutil <cmd>`;

sub Mail_Msg{
    $smtp = Net::SMTP->new( 'mail.company.com' );
    $smtp->mail( 'ALIAS@company.com' );
    $smtp->to( 'ALIAS@company.com' );
    $smtp->data();
    $smtp->datasend( "Subject:Job Failure\n" );
    $smtp->datasend( <<"EOF_MAIL" );

$body0
$body1

EOF_MAIL

    $smtp->datasend();
    $smtp->quit();
}
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