my ($a,$b);
while( $a=<F1>, $b= <F2>, $a or $b) {
  ...
}

##</code><code>##

use strict;
use warnings;
use Data::Dump qw/pp/;

open my $f1, "<", \ join "\n", 1..2;
open my $f2, "<", \ join "\n", 1..5;

while( defined (my $a=<$f1>) + defined (my $b=<$f2>) ) {
  $a .="";
  $b .="";
  chomp($a,$b);
  print "$a,$b\n";
}

##</code><code>##

1,1
2,2
,3
,4
,5