Virtually any templating system will be faster than that because it will compile the template once and use the compiled version to build the output in the loop. Here's how it would look if you used HTML::Template for example:

use HTML::Template;

my $TEMPLATE = HTML::Template->new_file($path_to_template);

open my $CSVIN, '<', $file;
foreach (<$CSVIN>) {

    #split CSV into usable format
    #the real script has about ten variables
    (my $input1, $input2, $input3, $file_out) = split(/,/, $_);

    open my $FHOUT, '>', $file_out;
    $TEMPLATE->param({$var1 => $input1,
                      $var2 => $input2,
                      $var3 => $input3, 
                      # ...
                     });
    print $FHOUT $TEMPLATE->output();
    close($FHOUT);

}    # end iteration through CSV
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Faster, and less code too!

-sam