use strict;

my $arrayVar;
$arrayVar->{"0,0"} = "a";
$arrayVar->{"1,0"} = "a";
$arrayVar->{"2,0"} = "a";
$arrayVar->{"3,0"} = "a";
$arrayVar->{"4,0"} = "a";

$arrayVar->{"0,1"} = "3";
$arrayVar->{"1,1"} = "2";
$arrayVar->{"2,1"} = "2";
$arrayVar->{"3,1"} = "3";
$arrayVar->{"4,1"} = "3";

$arrayVar->{"0,2"} = "aaa";
$arrayVar->{"1,2"} = "bbb";
$arrayVar->{"2,2"} = "aaa";
$arrayVar->{"3,2"} = "bbb";
$arrayVar->{"4,2"} = "bbb";

my @data;

# $arrayVar umwandeln in 2-dim. Array:
for (keys %$arrayVar) {
    my ($y, $x) = split /,/;
    $data[$y][$x] = $arrayVar->{$_};
}

# Array sortieren nach $spalte:
my @sorteddata = sort { $a->[0] cmp $b->[0] || $a->[1] <=> $b->[1] ||$a->[2] cmp $b->[2] } @data;

# $arrayVar neu aufbauen mit @sorteddata:
$arrayVar = {};
for my $y (0 .. $#sorteddata) {
    for my $x (0 .. $#{$sorteddata[$y]}) {
        $arrayVar->{"$y,$x"} = $sorteddata[$y][$x];
    }
}

# testen:
use Data::Dumper;
print Dumper \@sorteddata;