From perldoc -f crypt:

  When verifying an existing encrypted string you should use the
  encrypted text as the salt (like "crypt($plain, $crypted) eq
  $crypted"). This allows your code to work with the standard
  "crypt" and with more exotic implementations.
[download]

Works perfectly with htpasswd.

Update: Or you could try Apache::Htpasswd.

    $foo = new Apache::Htpasswd({passwdFile => "path-to-file",
                 ReadOnly   => 1}
                );
    # Check that a password is correct
    $pwdFile->htCheckPassword("zog", "password");
[download]