The White House, however, blocked it as it was not sure if it would actually help oust Bashar al Assad. There were questions also about which rebels to trust.
The Pentagon backing came out for the first time Thursday during a Senate committee hearing on the attack on the US mission in Benghazi last September.
"How many more have to die before you recommend military action?" Republican senator John McCain asked secretary of defence Leon Panetta.
McCain has long pushed for US intervention in Syria, citing the deaths of 60,000 people in the conflict over two years.
Did the Pentagon support the plan backed by Clinton and Petraeus, McCain asked Panetta and the chairman of the joint chiefs of staff Martin Dempsey. "We did," said both.
They didn't explain and McCain, who looked taken aback, didn't pursue as he was at the end of his allotted time. He later issued a statement noting the surprise admission. "The President overruled the senior leaders of his own national security team," McCain said.