This works for two, one or even zero elements.

use strict;
use warnings;

print
   map
   {
       qq{@{ [
          join
             q{;},
             @{ $_ } == 3
             ? ( @{ $_ } )
             : ( @{ $_ }, ( q{} ) x ( 3 - @{ $_ } ) ) ]
       }\n}
   }
   map { chomp; [ split m{;} ] }
   <DATA>;

__END__
a;3
b;2;3
c;5;4
d;6

f
[download]

The output.

a;3;
b;2;3
c;5;4
d;6;
;;
f;;
[download]

I hope this is useful.

Cheers,

JohnGG