Mr Obama's meeting with Mr Yang was arranged before the sea dispute
China and the US need to improve military-to-military contacts in order to avoid incidents such as the current maritime dispute, the White House says.
It released a statement urging better ties after President Barack Obama met Chinese Foreign Minister Yang Jiechi.
Tensions were raised after an unarmed US navy surveillance vessel was jostled by five Chinese vessels in the South China Sea last weekend.
A US official now says a destroyer has been sent to accompany the ship.
The unnamed official told AFP news agency such escorts would be provided "for the foreseeable future".
China has a key submarine base on Hainan island, 75 miles north of where Sunday's incident occurred.
The meeting between Mr Obama and Mr Yang had been arranged prior to the sea dispute.
But the issue loomed large over the talks. It was addressed obliquely by Mr Obama, the White House said, who called for better military contacts "to avoid future incidents" - and more directly by his National Security Adviser, James Jones, who also met Mr Yang.
SOUTH CHINA SEA TENSIONS
Territorial claims from China, the Philippines, Taiwan, Brunei, Vietnam and Malaysia overlap in resource-rich sea
Hosts some of the world's busiest shipping lanes
China says the US was in its Exclusive Economic Zone - but the two sides disagree on what activities are allowed in an EEZ
Meanwhile, in a strongly worded statement on Thursday, the Chinese defence ministry reiterated its position that the US ship had strayed into China's exclusive economic zone and demanded the US "take effective measures to prevent a recurrence", AP news agency reported.
Washington insists the US ship was operating in international waters.
The White House said Mr Obama also raised issues including the international financial crisis, North Korea, Afghanistan and Pakistan, Tibet and human rights.
On the economic crisis, the two "agreed that China and the US must work closely and urgently, as two of the world's leading economies, to stabilise the global economy by stimulating demand at home and abroad, and get credit markets flowing", the White House statement said.
"The president also emphasised the need to address global trade imbalances."
Mr Obama expressed hope for progress in the dialogue between Beijing and the Dalai Lama, Tibet's exiled spiritual leader.
Observers say this is a particularly touchy subject with China - which has been fuming at a resolution passed in the US House of Representatives condemning "repression" in Tibet.
In what was perhaps a reference to the Tibet issue, Mr Yang urged both sides to "shelve differences" that could not be immediately resolved, in a speech at the Institute for Strategic and International Studies.
"Confrontation hurts both sides," he said, according to AP.
When Mr Yang met US Secretary of State Hillary Clinton on Wednesday, he told her the US should "stop meddling in China's internal affairs through the Tibet issue", reported China's official Xinhua news agency.