my @data
while (my $line = <FILE>) {
   my @elements = split /,/, $line;
   push @data, \@elements;    # need to store as ref
}

@data = sort { $$a[2] cmp $$b[2]  or  $$a[0] <=> $$b[0] }
          @data;
# cmp and <=> are string and numerical comparison operators, 
# respectively; if the left hand arg is less than the right,
# they return -1, if equal, 0, and otherwise 1, so if the
# 3rd column of the array is the same, we get a 0, which 
# triggers the 'or' and the second comparison

open OUTFILE, ">$outfile" or die $!;
foreach my $item (@data) {
   print OUTFILE join ',', @$item;
   print OUTFILE "\n";
}