In a meeting with his Filipino counterpart, Defence Minister Richard Marles said Australia would increase bilateral activities in the contested territory as part of security efforts.
The commitments come as more than 2000 troops from both countries took part in military drills in the Philippines.
"Australia and the Philippines are close partners and friends. We share a firm commitment to a peaceful, stable and prosperous region where all countries are free to exercise their sovereignty consistent with international law," Mr Marles said in a statement.
"We recommitted to planning bilateral joint patrols in the South China Sea/West Philippine Sea and other areas of mutual interest. We committed to expanding some of our bilateral activities in the future to include other countries committed to sustaining peace and security in the region."
Tensions have been high in the South China Sea, with a Chinese ship blocking and firing a water cannon at a boat from the Philippines.
During the talks with the Philippines' national defence secretary Gilberto C Teodoro Jr, Mr Marles said Australia would look to elevate the relationship with the Asian nation to a strategic partnership.
Further formal talks will take place in Australia in 2024.
"We discussed the importance of all countries in the region exercising their agency in support of an Indo-Pacific region that is based on sovereignty, international law, and ASEAN centrality," Mr Marles said.
"Defence continues to make a significant contribution to our partnership. Under the enhanced defence cooperation program, we are working to broaden the scope of our cooperation and the complexity of our activities."
It comes as Prime Minister Anthony Albanese will become the first sitting prime minister to visit the Philippines in 20 years.
Mr Albanese will travel to the Philippines early next month and hold talks with President Ferdinand "Bongbong" Marcos Jr.
Mr Marles said the relationship between the two countries had the potential to expand.
"In amongst ASEAN countries, the Philippines itself is a country with whom we've had a very long relationship, actually a very strong personal relationship," he earlier told ABC Radio.
"We are now seeing a strategic dimension to the relationship and in that sense we see a greater strategic alignment between our two countries than we perhaps ever have in our history."
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