(CNN) -- Pakistan has decided to reopen supply routes that the United States and its allies have used for their troops in Afghanistan, U.S. Secretary of State Hillary Clinton said Tuesday.
Clinton also apologized for a "friendly fire" incident last November in which coalition forces killed 24 Pakistani soldiers at a checkpoint.
Clinton's announcement comes as representatives from the two nations discussed the reopening of ground supply routes into Afghanistan during meetings last weekend that included Gen. John Allen, the commander of U.S. and NATO troops in Afghanistan, said a senior U.S. official who wasn't authorized to speak publicly about the sensitive negotiations.
The talks had been stuck on two key issues -- Pakistan's demand to charge more per container shipped across its border, and Pakistan's demand the United States apologize for the friendly fire incident in November 2011.
U.S.-Pakistan relations plunged to an all-time low in the November incident, in which NATO fighter jets attacked a Pakistani checkpoint near the Afghan border.
The U.S. government expressed regret over the incident but had not issued a direct apology -- until Clinton's statement Tuesday.
"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's statement said. Clinton spoke with Pakistan's foreign minister by phone Tuesday morning, she said.
"The Foreign Minister and I were reminded that our troops -- Pakistani and American -- are in a fight against a common enemy. We are both sorry for losses suffered by both our countries in this fight against terrorists," Clinton said in the statement. "We have enhanced our counter-terrorism cooperation against terrorists that threaten Pakistan and the United States, with the goal of defeating Al-Qaida in the region."
Pakistan's ambassador to the United States, Sherry Rehman, said her country appreciated Clinton's statement and hopes "that bilateral ties can move to a better place from here."
"I am confident that both countries can agree on many critical issues, especially on bringing peace to the region," the ambassador said in a statement.
Regarding the U.S. apology, Qamar Zaman Kaira, Pakistan's minister for information and broadcasting, said that Pakistani leaders "are not calling this a big victory or someone else's defeat."
"The government and military of Pakistan has made them realize on principle that they should apologize to the Pakistani nation, and they did," Kaira said.
Kaira expressed concern about a domestic backlash by opposition parties about reopening the routes, but "hopefully Pakistani people will not listen to them," Kaira told CNN.
Meanwhile, the U.S. military will now pay Pakistan $1.1 billion it owes as part of the deal struck to reopen the NATO supply lines, according to U.S. officials who had knowledge of the agreement's details but weren't authorized to speak publicly.
The money is part of a U.S. military program called "coalition support funds," which reimburses the Pakistani military for counterterrorism efforts. The U.S. halted paying the bills from Pakistan as tension rose between the two countries.
The Pentagon will consult with Congress about paying the bills prior to paying Pakistan in full, according to one of the U.S. officials.
Pakistan will continue to press the U.S. administration to stop drone attacks, Kaira said.
Under Tuesday's announcements, Pakistan agreed not to impose any transit fee with the reopened routes, Clinton said in a statement.
Pakistan had been seeking $5,000 per truck as a condition of reopening the supply lines, U.S. officials said. The Pakistani routes offer a shorter and more direct route than the one NATO has been using since November that goes through Russia and other nations, avoiding Pakistan altogether.
It has cost the U.S. $100 million more a month to use the alternative northern routes.
Pakistan's Foreign Minister Hina Rubbani Khar told Clinton "that the ground supply lines (GLOC) into Afghanistan are opening," Clinton said in the statement.
"Pakistan will continue not to charge any transit fee in the larger interest of peace and security in Afghanistan and the region," Clinton said. "This is a tangible demonstration of Pakistan's support for a secure, peaceful, and prosperous Afghanistan and our shared objectives in the region."
The action will also help the United States and the NATO-led International Security Assistance Force conduct a planned drawdown of troops at a much lower cost, she said. "This is critically important to the men and women who are fighting terrorism and extremism in Afghanistan."
Before Clinton's apology on Tuesday, the United States had stopped short of such a gesture. President Barack Obama had offered condolences but stopped short of apologizing. Secretary of Defense Leon Panetta last month told Reuters that the United States was not amenable to an apology, and "I think it's time to move on."
Gen. John Allen, commander of U.S. and NATO forces in Afghanistan, said he welcomes the decision to reopen the supply lines "as a demonstration of Pakistan's desire to help secure a brighter future for both Afghanistan and the region at large," the NATO-led force said in a statement.
Per current practice, no lethal equipment will move into Afghanistan on the supply routes, except for equipment for the Afghan National Security Forces, Clinton said Tuesday.
Allen has traveled to Pakistan several times in recent weeks to meet with Gen. Ashfaq Parvez Kayani, Pakistan's chief of army staff, the NATO-led force said Tuesday, and continue building "the increasingly important and positive military-to-military relationship between Pakistan and ISAF."
Later Tuesday, Pakistan's Defense Committee of Cabinet, a group of top civilian and military leadership, announced it decided to reopen the routes after meeting at Prime Minister Raja Pervez Ashraf's house.
"The DCC stressed that, as recommended by the Parliament, Pakistan's future relations with the US must be based on mutual respect and mutual interest and conducted in a transparent manner," the statement said.
CNN's Chris Lawrence, Nasir Habib, Michael Martinez, Mike Mount and Jill Dougherty contributed to this report.