With more List::MoreUtils:

use strict;
use warnings;

use Test::More tests => 2;
use List::MoreUtils 'natatime';

my ($C, $R) = (4, 3);
my @list = 1..12;

my @AoA;
my $iter = natatime($C, @list);
while ( my @chunk = $iter->() ) {
    push @AoA, [@chunk];
}

is_deeply \@AoA, [[1 .. 4], [5 .. 8], [9 .. 12]];
is_deeply \@list, [1..12];
[download]

Updated: fixed two blunders in original post. Thanks LanX.

Update: This question reminds me of another recent node: How to Split on specific occurrence of a comma (where my response contains some CPAN List module refs)