Works for me when I pass it a reference to a simple array on Perl version 5.12.2:

use warnings;
use strict;
use Data::Dumper;

my $arr = [1..5];
shuffle($arr);
print Dumper($arr);

sub shuffle
{
    my $array = shift;
    my $i = @$array;
    while ( --$i )
    {
        my $j = int rand( $i+1 );
        @$array[$i,$j] = @$array[$j,$i];
    }
}

__END__

$VAR1 = [
          3,
          5,
          4,
          1,
          2
        ];
[download]

What version of Perl? How do you call the sub?

See also List::Util::shuffle