You've identified the solution I'd choose (HTML::Parse or another module), but in the absence of that, you can get a pretty good solution with split:

my @chunks = split(/<!--#include virtual="([^"]+)" -->/, $data);
while (@chunks) {
    # ought to splice here
    my ($html, $inc) = (shift @chunks, shift @chunks);

    # print $html to file
    # include $inc if possible
}
[download]

Beware that @chunks may contain an odd number of elements, so $inc may be empty on the last iteration.

It's not the *best* way to do it, but it's one way to do it.