Obama also warned that Washington and other international allies would end their support of the world's youngest nation if any party attempted a military coup, amid fears the country was on the brink of civil war.
Three US military Osprey aircraft came under fire as they headed to the rebel-held city of Bor in Jonglei state to help evacuate Americans, the Pentagon said.
All four wounded service members were in "stable condition," it added. The targeted Bell Boeing CV-22 Ospreys are hybrid tiltrotor aircraft that can take off vertically like a helicopter but resemble a normal plane in flight.
"He underscored that South Sudan's leaders have a responsibility to support our efforts to secure American personnel and citizens in Juba and Bor," a White House statement said.
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Obama separately participated in a secure call about the situation in South Sudan with National Security Adviser Susan Rice, her deputies Tony Blinken and Ben Rhodes, as well as White House Senior Director for African Affairs Grant Harris, also a member of the president's national security team.
"More broadly, the president underscored the urgency of helping to support efforts to resolve the differences within South Sudan through dialogue," the White House added.
It called for an end to the recent surge of violence that has killed at least 500 people in the capital Juba alone in six days of fighting.
"Any effort to seize power through the use of military force will result in the end of longstanding support from the United States and the international community," the White House said.
On Wednesday, the United States deployed 45 combat-equipped troops to the country to protect its embassy and American personnel.
Kenya and Uganda have also sent in troops to help evacuate stranded nationals.