Was this at night? If it was daylight, then I'm puzzled. If you know you're over Java (and you'd have to be very very lost to not know at least that much*) just head straight north and pretty soon you'll reach the coast (Java is long and skinny). Then turn left, and pretty soon you'll either reach Jakarta or run out of island (there's very little of Java that's west of Jakarta), in which case a 180 will take you to Jakarta. Even at night this should be doable, as coastlines should show up pretty well. The ony way it wouldn't work is in case of complete overcast; there's some pretty tall mountains around, so you probably don't want to let down blind if you don't know where you are.
*: if you're sufficiently lost that you could conceivably be over Sumatra (not very far from Java), the same trick still works -- Sumatra is oriented NW-SE, so the coastline has an entirely different orientation, and if you start near the south coast, it could take you very long to reach the north coast; either way a compass and watch should be enough to establish pretty quickly whether you're over Sumatra or Java.