File 1 example:- 

WL,BL,Die1
WL0,BL0,1708
WL0,BL1,1708
WL0,BL2,1708
WL0,BL3,1931
WL0,BL4,1931

File 2 example:- 

WL,BL,Die 2
WL0,BL0,1708
WL0,BL1,1931
WL0,BL2,1708
WL0,BL3,1931
WL0,BL3,1708

Output after script:- 

WL,BL,Die1, Die2
WL0,BL0,1708,1708
WL0,BL1,1708,1931
WL0,BL2,1708,1708
WL0,BL3,1931,1931
WL0,BL4,1931,1708

My script:- 

#!/usr/bin/perl 

#Copy Die2 as Output file
use File::Copy; 
copy ("Die2_10k.txt","CombineDie1Die2.txt") or die "copy failed: $!"; 

#Open Die1 Input file 
open (Label, "Die1_10k.txt") or die "can't open Die1: $!"; 

#Search and replace using 1 liner command 
while (<Label>) { 
	$replace = $_; 
	chomp ($replace); 
	@temp = split (/,/, $replace); 
	$search = $temp[0].",".$temp[1];  
	
	$command_line = "perl -pi\.bak -e s\/".$search."(?=,)\/".$replace."\/g\; CombineDie1Die2.txt"; 
	
	system ($command_line); 
}