If you are only choosing two elements at a time, a simple solution may be best:

my @arr = (1..100);
foreach my $i (0..@arr-1) {
   foreach my $j (0..@arr-1) {
      next if $i == $j;
      print "$arr[$i],$arr[$j]\n";
   }
}
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if r > 3 or so, tye's solution is good for more general cases.