Obama used an address to US and Filipino troops in Manila to again voice concern over the increasingly tense maritime rows between China and US allies in the region, an issue that has dominated his four-nation trip.
"We believe that nations and peoples have the right to live in security and peace, to have their sovereignty and territorial integrity respected," Obama said.
"We believe that international law must be upheld, that freedom of navigation must be preserved and commerce must not be impeded. We believe that disputes must be resolved peacefully and not by intimidation or force."
The Philippines has been embroiled in one of the highest-profile territorial disputes with China, over tiny islets, reefs and rocks in the South China Sea.
China claims nearly all of the South China Sea, which is believed to contain huge deposits of oil and gas, even waters and formations close to its neighbours.
The Philippines, which has one of the weakest militaries in the region, has repeatedly called on long-time ally the United States for help as China has increased military and diplomatic pressure to take control of the contested areas.
The Philippines and the United States signed an agreement on Monday that will allow a greater US military presence on Filipino bases.
Obama pledges support
And Obama sought on Tuesday to reassure the Philippines that the United States would back its ally in the event of being attacked, citing a 1951 mutual defence treaty between the two nations.
"This treaty means our two nations pledge, and I am quoting, 'our common determination to defend themselves from external armed attacks'," Obama said.
"And no potential aggressor can be under the illusion that either of them stands alone. In other words, our commitment to defend the Philippines is ironclad. The United States will keep that commitment because allies will never stand alone."
Nevertheless, Obama did not specifically mention coming to the aid of the Philippines if there was a conflict over the contested South China Sea areas, as his hosts had hoped.
On the first leg of his Asian tour in Tokyo, Obama had made such a pledge of support to Japan, which is locked in another dispute with China over rival claims to islands in the East China Sea.
Obama's nuanced position on the Philippines was part of a tight-rope act he had tried to perform during his trip - reassuring allies wary about China's perceived increased hostility while not antagonising the leadership in Beijing.
While offering pledges of protection to Japan and the Philippines, Obama also insisted the United States was not seeking to counter or contain China.
But an editorial in the state-run China Daily newspaper Tuesday signalled Chinese authorities did not believe Obama's assurances were genuine.
"It is increasingly obvious that Washington is taking Beijing as an opponent," the editorial said.
"With Obama reassuring the US allies of protection in any conflict with China, it is now clear that Washington is no longer bothering to conceal its attempt to contain China's influence in the region."
The editorial warned against believing Obama's "sweet promises" of a new, constructive relationship between the United States and China, and instead outlined what it described as a "grim geopolitical reality".
"Ganging up with its troublemaking allies, the US is presenting itself as a security threat to China," it said.
However, reflecting the difficulties of Obama's balancing act, there were also complaints in the Philippines that he had not offered explicit support in the event of a conflict over the contested South China Sea areas.
"No firm commitment from US to defend PH," said the front-page headline of the Philippine Daily Inquirer after Obama met president Benigno Aquino on Monday but did not pledge South China Sea backing.
And after Obama made his speech on Tuesday, Aquino ally Senator Antonio Trillanes said the Philippine leadership was now fully aware that US troops would not join Filipino troops in a potential conflict with China over the South China Sea.
"So at least it's very clear that there are no false expectations and we just have to deal with that by ourselves," Trillanes said.
US President Barack Obama delivers remarks to US and Philippine troops at Fort Bonifacio in Manila. (Noel Celis, AFP)