Best guess at what you want:

file1.txt

needle:filed12:field13:field14:field15:field16
haystack:filed22:field23:field24:field25:field26
lost:filed32:field33:field34:field35:field36

file2.txt

Line,one,fff,ggg,hhh
line,two,hidden,haystack,in,open
Line,three,just,some,junk
line,four,has,needle,here
more,ending,junk.
[download]

code:

use strict;
use warnings;

my @one_lines;
open my $one,"<","file1.txt" or die $!;

while (<$one>){
   chomp;
   my (@fields)=split /:/;
   push @one_lines,{KEY=>$fields[0], F4=>$fields[3]};
}
close $one;
#------
open my $two,"<","file2.txt" or die $!;

while (defined(my $line=<$two>)){
   chomp $line;
   my @fields = split /,/,$line;
   my $matched_line={F4=>""};
   for (@one_lines){
     next unless $line=~m/$_->{KEY}/;
     $matched_line=$_;
     last;
   }
   $fields[5] = $matched_line->{F4} if $matched_line->{F4};
   print join(",",@fields),"\n";
}
close $two;
[download]

Output:

>perl 11109568.pl
Line,one,fff,ggg,hhh
line,two,hidden,haystack,in,field24
Line,three,just,some,junk
line,four,has,needle,here,field14
more,ending,junk.
[download]

Redirecting output to "file3" is left as an exercise.

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