Clinton said her Pakistani Foreign Minister Hina Rabbani Khar, during a telephone talk, "informed me that the ground supply lines into Afghanistan are opening".
Islamabad had long demanded that US must apologise for the air raid that killed 24 Pakistani army personnel before it would re-open the supply routes to Afghanistan.
"Foreign Minister Khar and I acknowledged the mistakes that resulted in the loss of Pakistani military lives," Clinton said in a statement.
"We are sorry for the losses suffered by the Pakistani military. We are committed to working closely with Pakistan and Afghanistan to prevent this from ever happening again," Clinton said.
"Pakistan will continue not to charge any transit fee in the larger interest of peace and security in Afghanistan and the region. This is a tangible demonstration of Pakistan's support for a secure, peaceful, and prosperous Afghanistan and our shared objectives in the region." (MORE)