First, always use strictures (use strict; use warnings;). They will give you an early heads up about many silly errors and typos.

Use the three parameter version of open and check the result. It's more secure, the intent is clearer and checking the result saves a heap of time debugging silly errors.

Avoid slurping files (@file = <MYFILE>;). It doesn't scale well. It doesn't generally improve performance and it doesn't generally help code clarity.

push (@sort ,"@split[2]\t@split[1]\t@split[3]\t@split[0]\t@split[4]");
[download]

is better written:

push (@sort ,"$split[2]\t$split[1]\t$split[3]\t$split[0]\t$split[4]");
[download]

but is much clearer using an array slice:

push @sort, join "\t", @split[1, 2, 3, 4, 0];
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However, in Perl when you think 'unique', you should generally then think 'hash'. Consider:

use strict;
use warnings;

my $data = <<DATA;
2009-01-08 09:29:19    ABCDEF    943973    MS08-011    Security Update
+ for Microsoft Works Suite 2005 (KB943973)
2009-01-08 09:29:19    ABCDEF    943973    MS08-011    Security Update
+ for Microsoft Works Suite 2005 (KB943973)
2009-01-08 09:29:19    ABCDEF    951944    MS08-055    Security Update
+ for the 2007 Microsoft Office System (KB951944)
2009-01-08 09:29:19    ABCDEF    953432        Update for Microsoft Of
+fice Outlook 2003 (KB953432)
2009-01-08 09:29:19    ABCDEF    954038    MS08-051    Security Update
+ for 2007 Microsoft Office System (KB954038)
2009-01-08 09:29:19    ABCDEF    954326    MS08-052    Security Update
+ for the 2007 Microsoft Office System (KB954326)
2009-01-08 09:29:19    ABCDEF    956391        Cumulative Security Upd
+ate for ActiveX Killbits for Windows 2000 (KB956391)
2009-01-08 09:29:20    ABCDEF    956828    MS08-072    Security Update
+ for the 2007 Microsoft Office System (KB956828)
2009-01-08 09:29:20    ABCDEF    956828    MS08-072    Security Update
+ for the 2007 Microsoft Office System (KB956828)
2009-01-08 09:29:20    ABCDEF    957832        Update for Microsoft Of
+fice Outlook 2003 Junk Email Filter (KB957832)
2009-01-08 09:29:22    ABCDEF    958439    MS08-074    Security Update
+ for the 2007 Microsoft Office System (KB958439)
2009-01-08 09:29:22    ABCDEF    958439    MS08-074    Security Update
+ for the 2007 Microsoft Office System (KB958439)
DATA

open my $inFile, '<', \$data;

my %entries;

while (<$inFile>) {
    my ($date, $time, $endpoint, $kbid, $id, $title) =
        /(\S+)\s+ (\S+)\s+ (\S+)\s+ (\S+)\s+ (\w+-\d+\s+)? (.*)/x;

    $id ||= '';
    $entries{$kbid} = {
        date     => $date,
        time     => $time,
        endpoint => $endpoint,
        id       => $id,
        kbid    =>  $kbid,
        title    => $title,
        };
}
close $inFile;

print join ("\t", @{$_}{qw(id kbid title endpoint date)}), "\n"
    for sort {$a->{id} cmp $b->{id} or $a->{kbid} <=> $b->{kbid}} valu
+es %entries;
[download]

Prints:

    953432    Update for Microsoft Office Outlook 2003 (KB953432)    A
+BCDEF    2009-01-08
    956391    Cumulative Security Update for ActiveX Killbits for Wind
+ows 2000 (KB956391)    ABCDEF    2009-01-08
    957832    Update for Microsoft Office Outlook 2003 Junk Email Filt
+er (KB957832)    ABCDEF    2009-01-08
MS08-011        943973    Security Update for Microsoft Works Suite 20
+05 (KB943973)    ABCDEF    2009-01-08
MS08-051        954038    Security Update for 2007 Microsoft Office Sy
+stem (KB954038)    ABCDEF    2009-01-08
MS08-052        954326    Security Update for the 2007 Microsoft Offic
+e System (KB954326)    ABCDEF    2009-01-08
MS08-055        951944    Security Update for the 2007 Microsoft Offic
+e System (KB951944)    ABCDEF    2009-01-08
MS08-072        956828    Security Update for the 2007 Microsoft Offic
+e System (KB956828)    ABCDEF    2009-01-08
MS08-074        958439    Security Update for the 2007 Microsoft Offic
+e System (KB958439)    ABCDEF    2009-01-08
[download]