Well, as long as you can be sure its the last line, you can find out where the last line is and use truncate, and then append the new last line. I have an example here where I just replace the whole __DATA__ portion:

#!/usr/bin/perl -w
use strict;

my $new = "new text here!\n";

my $data_pos = tell DATA;

open SELF, "+<$0" or die "open $0: $!\n";

truncate SELF, $data_pos or die "truncate: $!\n";

seek SELF, 0, 2 or die "seek: $!\n"; # append now.

print SELF "$new" or die "print: $!\n"; # just in case

close SELF or die "while closing $0: $!\n";

__DATA__
this is the stuff to replace
[download]

Be aware that this has a race condition if two copies of the script are run at once. The race condition can be eliminated by adding an flock after open as long as it can be gaurenteed that the script (before the __DATA__) will not be modified while it runs.

update: (more) minor typos fixed, die check added, (more recently) rephrased to actually explain algorithm.