Bali and Java are separated by the Bali Strait, a narrow stretch of water only 3km across. Ferries operate 24 hours a day and can be accessed simply by arriving and buying a ticket. Cars, trucks and motorbikes can also roll up and get on without too much of a hitch.
Onward transport is available in Java, assuming you have not arranged it. Most of the local tour buses from Bali operate out of the Ubung terminal in NW Denpasar, with pick up points in Tabanan and Negara. Large quality AC buses will take you from there, across to Java and to points including Yogyakarta and Jakarta. There are also tourist buses and bus & train combinations that operate from the main towns in the island. The price of the ferry crossing is included in the bus ticket.
The port in west Bali is Gilimanuk, its counterpart in Java is Ketapang. The crossing takes just 20 minutes. You can buy a ticket on foot as you get on the boat (3,300rp and 2,200 for children). Motorbikes are 9,000-20,000rp including the rider and cars are 55,000rp including the passengers.
In Ketapang you will see the Banyuwangi Baru train station is only 100 meters north from the terminal. This will take you to Surabaya, Probolinggo (for Mt. Bromo) and Yogyakarta. Just 8km south of Ketapang is the town of Banyuwangi (means water that smells good). Catching a bemo to Banyuwangi will get you to the main bus station where you can find buses to major cities in Java.
Most car rental places in Bali do not like you to take their vehicles to Java, because they have very little chance of getting them back if they are stolen. People have said the police will ask for 50% of the price of the vehicle to get it back, They will also try to impound the vehicle in a road accident. If you do take your car to Java drive carefully and don’t hang around for the police to find a reason to haul you in.
If you do ride a long distance bus across Java, do not accept drinks from other passengers. Indonesians themselves will tell you this, due to the fact that people have been drugged, especially during Idul Fitri.
Travelling on a new AC across Java can be enjoyable. you may make new acquaintances with locals, stop at local food places and see more of the country than flying. Its also a very affordable way to go. The modern AC buses will have a toilet on board and assigned seating, unlike the non-AC cattle buses that stop for people along the way. Most travel agents in Bali will be able to hook you up with long distance bus tickets as will the Perama offices.