Simple solutions are probably just a regular expression:

$varalias =~ s/=.*//;  # Delete everything(.*) from the equals on
$vartarget =~ s/"$//;  # Delete the quote at the end($)
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As a note, your regular expression scares the willies out of me, a strong case for Death to Dot Star!. You probably mean to do something like this:

# If able to delete the stuff(.*) between the beginning
# of the line(^) and the word 'alias' and one-or-more spaces(\s+)
# found after that ...
if (s/^.*?alias\s+//)
{
     # Extract the 1st, 5th and 7th "words"
     my ($varalias, $varsource, $vartarget)
           = (split(' '))[1,5,7];

     # Then whatever...
}
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Here's a few general tips which can help you simplify your program.

Your print to OUT just screams out for a "here document" style approach, where you can put a whole bunch of stuff right in your program and save yourself having to quote it properly. As a bonus, you don't have to "escape" your quote marks, like you have done:

print OUT <<END_HTML;
<FOO>
<FOO>$varsource
<FOO>
<FOO>$vartarget
<FOO>
<FOO>
END_HTML
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Also, you can increment a variable with the ++ operator, like so: $i++ and that is the same as $i = $i + 1 but is much shorter.

Don't forget to indent, either. Not indenting is a major Faux Pas, kind of like arrivng at work without a shirt on. You can do it, but people look at you funny. Whenever you open braces, kick it in a tab stop. Some editors can do this for you automatically, if you're feeling Lazy. Example:

if ($something)
{
      some_code();

      if ($something_else)
      {
             some_other_code();
      }
}
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