"Secretary Clinton did a great job negotiating the re-opening of supply routes from Pakistan to Afghanistan," McCain wrote on his official Twitter account on Thursday.
The incident occurred when American and NATO forces mistook Pakistani forces for insurgent fighters and opened fire. In retaliation, Islamabad closed off supply routes in Pakistan that have been used by coalition forces in neighboring Afghanistan.
In a conversation with Pakistani Foreign Minister Hina Rabbani Khar on Tuesday, Clinton personally apologized for the attack.
"We are both sorry for losses suffered by both our countries in this fight against terrorists," Clinton said in a statement released that day on their conversation.
While the White House and the Pentagon have repeatedly expressed their regret for the air raid, no one from the Obama administration had formally or informally apologized for the attack until Tuesday.
A formal U.S. apology was one of several demands Islamabad made as a precursor to allowing American and coalition forces access to the key supply routes.
Defense Secretary Leon Panetta welcomed Pakistan's decision, indicating it was a sign of an improving partnership between Islamabad and Washington, but he did not issue an apology of his own.
With the routes now open, U.S. and NATO forces can begin moving the mountains of weapons and equipment out of Afghanistan, in preparation for the complete American withdrawal from the country in 2014.