Use eof to determine if the next read will fail due to end of file. Here's an example. This is just a demonstration rather than a refactoring of your code. But the technique would prove to adapt to your code in a straightforward way.

while( my $line = <DATA> ) {
  print $line if $. % 5 == 0 || eof(\*DATA);
}



__DATA__
line one
line two
line three
line four
line five
line six
line seven
line eight
line nine
line ten
line eleven
[download]

Output:

line five
line ten
line eleven
[download]

Update: Here is a revision of your original code that handles end-of-file correctly without duplicating your printf statements:

my ($sum, $count) = (0,0);

while (<DATA>) {
  $sum += $_;
  $count++;
  if ($count == 5 || eof(\*DATA) ) {
        printf "Sum: %4d, count: %2d, mean: %5.1f\n", 
            $sum, $count, $sum/$count;
        $sum = 0;
        $count = 0;
    }
}

__DATA__
61
23
30
444
368
438
467
44
812
430
992
469
[download]

I provided this to show that a solution that eliminates code repetition needn't be complicated or illegible. I literally changed only two things; one, removed 'printf' outside of the loop; and two, added || eof(\*DATA) to your if conditional.

Philosophically your goal is worthwhile. Today, perhaps it's just a printf. Tomorrow it could grow to a few lines. And the next day you might alter the format string and parameters of the printf. Suddenly you find yourself needing to make the change in two places instead of one, and possibly get one of those changes wrong. It just makes sense; if you can avoid repetition without making the code illegible or grossly inefficient, seek to do so.