Extending the replies above:

re Re: Unknown numbers show up: An alternate to Athanasius' look-ahead assertion would be to insert an anchor in $replace (which would also require you to use a "quote-like" operator, qr/ ... /;)
          ...thus:  $search = qr/$temp[0],$temp[1]$/;

You might also want to read perldoc perlretut and/or perldoc perlre for a better understanding of the impact your quotes, dots, etc have on Ln 18,

And, re flexvault's note: definitely, don't call another instance of Perl to execute your  s/// and especially, don't call it in a loop. Do rewrite it so the substitution is executed without system..... That's left as an exercise for the Seeker.
I'm not sure that writing to a third file is necessary, though... but that may well be merely my blindspot.

#!/usr/bin/perl 
use 5.010;

# 1123214
#Copy Die2 as Output file
 
use File::Copy; 
copy ("Die2.txt","CombineDie1Die2.txt") or die "copy failed: $!"; 

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

#Search and replace using 1 liner command 
while (<Label>) { 
    $replace = $_; 
    chomp ($replace); 
    @temp = split (/,/, $replace); 
    $search = qr/$temp[0],$temp[1]$/;    # using an anchor
    print "\t search is $search";
    $command_line = "perl -pi\.bak -e s\/$search/$replace/g\; CombineD
+ie1Die2.txt";
         # NB the removal of numerous dots, quotes and backslashes
    system ($command_line); 
}
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