There is always QF825 bia BNE. It departs Darwin at 13:40 and should make reasonable connections to SYD.
Or you could take the international extension of QF82 departing Darwin at 05:30 (it comes from SIN overnight) on a 767-300 to Adelaide and connect to SYD from there. Other flights via Adelaide at 07:30 (Thur, Sat) and 13:00 daily.
Besides, you get more SC's and points by going via BNE or ADL

.