Have you seen “Update 4” at the original story link...
Notice the timeline moving forward from here...
“11 p.m. (5 p.m. ET): Just ahead of the weekly meeting with Defense Secretary Leon Panetta and Chairman of Joint Chiefs Martin Dempsey, White House National Security Advisor Tom Donilon tells President Obama of the attack and the fire at the main villa. The president is updated several times throughout the evening.”
At the exact time of the attack 3:30-3:40pm, Obama was at Walter Reed. I have a hard time believing Obama wasn’t notified immediately.