The statement is a commitment to international law and promoting regional economic growth.
Prime Minister Malcolm Turnbull says the Jakarta talks have been successful on many fronts.
"Today is a historic moment in Jakarta Mr President. In recent times we have not had as much to do with each other, we have not worked together as much as we ought to and as much as we will in the future," Mr Turnbull said.
Mr Turnbull's visit to Jakarta comes just a week after Indonesian President Joko Widodo was hosted in Australia, and the Australian PM praised Indonesia as its best ally in the war against violent extremism.
"In that war against Islamist terrorism, extremism, our best allies, our most important allies are Muslim leaders like Joko Widodo," said Mr Turnbull.
The two nations are also standing side by side in their quest to sign a free trade agreement by the end of the year.
"We are not trading enough with Indonesia and both sides recognise that," said Mr Turnbull.
Turnbull rules out joint South China Sea patrols
Mr Turnbull earlier ruled out Australia and Indonesia conducting joint-patrols in the South China Sea, after reports surfaced both countries were contemplating the idea.
“We are not going to undertake any actions which would increase tensions in the South China Sea,” he said.
Before his recent visit to Australia, President Joko Widodo hinted at joint patrols in the sea in the future, an issue he highlighted he planned to raise with Mr Turnbull.
Asked about their behind door discussions on Tuesday the prime minister said he was “being very careful” in discussing the complex issue, but said Australia was “certainly determined” to work more closely with Indonesia.
“Our commitment is to increase our cooperation with each other in terms of maritime security," he said.
"We talk about more collaboration, more coordination, but it has not been taken any further than that.
“But that is the limit of what I can say and that is the limit of any discussions.
- with AAP
