use strict;
use warnings;

# our data in arrays
my @rect_x = (3,2,4,0,3,0,4,0,3,2,0,4);
my @rect_y = (0,0,0,1,1,0,3,3,3,3,2,2);

# create an array 0,1,2,3,....as long as my data is
my @unsorted = 0..$#rect_x;

# these indexes we sort by Y and then reverse sort by X
my @sorted = sort { $rect_x[$b] <=> $rect_x[$a] } 
             sort { $rect_y[$a] <=> $rect_y[$b] } 
             (@unsorted);

my $n = 0;
for my $i (@sorted){
    print "$n $i \t $rect_x[$i] $rect_y[$i]  \n";
        ++$n;
}
[download]

yields:

$ perl lowest_sort.pl 
0 2       4 0  
1 11      4 2  
2 6       4 3  
3 0       3 0  
4 4       3 1  
5 8       3 3  
6 1       2 0  
7 9       2 3  
8 5       0 0  
9 3       0 1  
10 10     0 2  
11 7      0 3
[download]