More than 100 militants were killed in airstrikes by the US warplanes at an al-Qaida training camp in Syria, the Pentagon has said.
A Pentagon spokesperson, Navy Capt Jeff Davis, said the camp in Idlib province had been active since at least 2013.
"The removal of this training camp disrupts training operations and discourages hard-line Islamist and Syrian opposition groups from joining or cooperating with al Qaeda on the battlefield," Davis said.
The Syria strike was carried out by one B-52 bomber and an undisclosed number of US aerial drones.
It happened at about noon Washington time on Thursday, less than 24 hours after a combination of B-2 stealth bombers and drones struck two military camps in a remote part of Libya, killing 80 to 90 Islamic State militants.
Obama specifically authorised the Libya strike. It was not immediately clear whether the Syria strike required his direct approval.
The militants killed in the Syria attack were described by one defense official as "core" al Qaeda members, among a number who had moved to Syria early last year to establish a foothold.
The official distinguished these militants from members of the group formerly known as the Nusra Front, which is an al Qaeda affiliate in Syria.
Davis said Thursday's attack capped a string of successful strikes against al Qaeda this month. He said the strikes have killed more than 150 members of the group since January 1.
They include Mohammad Habib Boussadoun al-Tunisi, an external operations leader, killed last Tuesday, he said.
"These strikes, conducted in quick succession, degrade al-Qaida's capabilities, weaken their resolve, and cause confusion in their ranks," Davis said.