Hi,
better use split for this type of stuff. It lets you specify the number of fields that you want to read and fills up the last one (field 6 here) with the rest of the line.

#!/usr/bin/perl
use strict;
use warnings;

open (DATA,"</var/log/messages") || die 'Unable to open log file';
open (TMP, ">/tmp/messages.csv") || die 'Unable to write to file';

while (<DATA>) {
    chomp;
    my (@cols) = split(/\s+/, $_, 6);
    print TMP join(',',@cols), "\n";
}

close TMP;
close DATA;

__DATA__
Oct  1 13:23:25 smoothwall-swe3 kernel: Allocating PCI resources start
+ing at 10000000 (gap: 08000000:f6c00000)
Oct  1 13:23:25 smoothwall-swe3 kernel: Built 1 zonelists
Oct  1 13:23:25 smoothwall-swe3 kernel: Kernel command line: BOOT_IMAG
+E=SmoothWall ro root=804 ramdisk_size=8192 no-scroll panic=30
Oct  1 13:23:25 smoothwall-swe3 kernel: Enabling fast FPU save and res
+tore... done.
Oct  1 13:23:25 smoothwall-swe3 smoothd: Loading Plugins for Module "/
+usr/lib/smoothd/sysinstall.so
[download]

prints:

Oct,1,13:23:25,smoothwall-swe3,kernel:,Allocating PCI resources starti
+ng at 10000000 (gap: 08000000:f6c00000)
Oct,1,13:23:25,smoothwall-swe3,kernel:,Built 1 zonelists
Oct,1,13:23:25,smoothwall-swe3,kernel:,Kernel command line: BOOT_IMAGE
+=SmoothWall ro root=804 ramdisk_size=8192 no-scroll panic=30
Oct,1,13:23:25,smoothwall-swe3,kernel:,Enabling fast FPU save and rest
+ore... done.
Oct,1,13:23:25,smoothwall-swe3,smoothd:,Loading Plugins for Module "/u
+sr/lib/smoothd/sysinstall.so
[download]

Regards,
svenXY