Why not use a hash? This is where they shine:

## I don't know how you're getting values for $i, $j, $value
$hash{$i}{$j} = $value;
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Update2: To print:

foreach $i (keys %hash) {
   foreach $j (keys %{ $hash{$i} }) {
      print $i, $j, $hash{$i}{$j}, "\n";
   }
}
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Hope this works for you.

Update1: If you insist on arrays, however, this will also work (but is more work):

push @array, "$i:$j:$value";

## to print:
foreach (@array) {
   print join (' ', split ":");
}
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@a=split??,'just lose the ego and get involved!';
for(split??,'afqtw{|~'){print $a[ord($_)-97]}