Spawning another copy of Perl to handle a search and replace feels completely wrong. Since your files are "in sync" you can simply read them in parallel and generate the output as you go. The following code uses a trick described in I know what I mean. Why don't you? to make a self contained example. You should replace the open statements for production code.

#!/usr/bin/perl
use strict;
use warnings;
 
my $File1 = <<FILE;
WL,BL,Die1
WL0,BL0,1708
WL0,BL1,1708
WL0,BL2,1708
WL0,BL3,1931
WL0,BL4,1931
FILE
my $File2 = <<FILE;
WL,BL,Die 2
WL0,BL0,1708
WL0,BL1,1931
WL0,BL2,1708
WL0,BL3,1931
WL0,BL3,1708
FILE

open my $in1, '<', \$File1;
open my $in2, '<', \$File2;

while (my $line1 = <$in1>) {
    chomp $line1;
    defined (my $line2 = <$in2>) or last;
    
    print $line1, ',', (split ',', $line2)[-1];
}
[download]

Prints:

WL,BL,Die1,Die 2
WL0,BL0,1708,1708
WL0,BL1,1708,1931
WL0,BL2,1708,1708
WL0,BL3,1931,1931
WL0,BL4,1931,1708
[download]