No need for two loops at all, much less a temporary file:

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

my $in = "c:/tmp.txt";
open( my $ifh, "<", $in ) or die $!;
my $out = "c:/final.txt";
open( my $ofh, ">", $out ) or die $!;

my %hash;
while( <$ifh> ) {
    chomp;
    next
        if  ! m/^\s+\d/;
    s/^\s+//g;
    s/\s+$//g;
    s/\s+/,/g;
    my $key = join ',', ( split /,/ )[ 1, 2, 3, 4 ];
    print $ofh $_, "\n"
        if  ! $hash{$key}++;
}
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Use while(<>) not foreach(<>) as the latter loads the whole file into RAM.