You need to sort the two columns independently then put them back together. Note that the following code assumes that both columns contain the same number of entries:

use warnings;
use strict;

my @firsts;
my @seconds;

while(<DATA>) {
    chomp;
    my($val1,$val2) = split /,/;
    
    push @firsts, $val1;
    push @seconds, $val2;
}

@firsts = sort {$a <=> $b} @firsts;
@seconds = sort {$a <=> $b} @seconds;

my @sorted;

push @sorted, [$firsts[$_], $seconds[$_]] for 0..$#firsts;

print "$_->[0], $_->[1]\n" for @sorted;

__DATA__
10,20
30,10
20,70
70,80
40,90
90,100
50,50
[download]

Prints:

10, 10
20, 20
30, 50
40, 70
50, 80
70, 90
90, 100
[download]