The BBC's Orla Guerin says these much-needed supplies could soon be on the move again, following a long-awaited "sorry" from the US;
Pakistan will reopen crucial supply routes to Nato-led forces in Afghanistan after the US apologised for killing 24 of its soldiers in November, Washington and Islamabad have said.
The decision will save the US hundreds of millions of dollars in as it prepares to withdraw from Afghanistan.
Pakistan has said it hopes the move will improve relations with the US and other Nato countries.
The Pakistani Taliban promptly threatened to attack the convoys.
US Secretary of State Hillary Clinton announced the decision after a telephone conversation with her Pakistani counterpart, Hina Rabbani Khar.
"I offered our sincere condolences to the families of the Pakistani soldiers who lost their lives," she said in the statement.
The seven month-long row over supply lines have been hugely damaging to relations between Pakistan and the US, with both sides unwilling to back down.
It began in November last year when two dozen Pakistani soldiers were killed as US air strikes hit two posts on the Afghan border.
At the time, Afghan officials said that Nato forces had been retaliating for gunfire from the Pakistani side of the volatile border, but Pakistan rejected that claim.
The supply route through Pakistan is crucial to the United States as it prepares to pull all combat troops out of Afghanistan by 2014.
Reports suggest the US may now release over $1bn in funding to Pakistan's military.
In a statement, Ms Clinton said: "Foreign Minister Khar and I acknowledged the mistakes that resulted in the loss of Pakistani military lives.
"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."
Islamabad confirmed it would not raise transit fees when the lines re-open.
US officials say the existing charge of $250 (£160) per truck will not change - Washington had baulked at a Pakistani demand for $5,000 per container to let supplies flow again.
The BBC's Kim Ghattas says Washington had resisted saying sorry as there is deep anger among Americans about the death of US soldiers in Afghanistan from attacks by militant groups with alleged connections to Pakistan's ISI intelligence agency.
Shortly before Tuesday's announcement, Pakistani Prime Minister Raja Pervez Ashraf said the issue had damaged his country's relations with the US, as well as the 49 other Nato member states.
After the US apology Pakistan's ambassador to Washington Sherry Rehman said she hoped bilateral relations between the two countries could move to a "better place".
"I am confident that both countries can agree on many critical issues, especially on bringing peace to the region," she added.
During the dispute the US reduced its reliance on Pakistan by using a more costly route through Central Asia.
General John Allen, the US commander of Nato troops in Afghanistan, said the decision to open the supply lines was "a demonstration of Pakistan's desire to help secure a brighter future for both Afghanistan and the region at large".
Gen Allen had held talks in Islamabad twice in the last six days.
In April, Pakistani lawmakers approved new guidelines for ties with the US, but demanded that the country provide an unconditional apology for the November attack, and stop drone strikes.
The standoff cast a diplomatic shadow over a Nato summit two months ago in Chicago where correspondents said US President Barack Obama snubbed his Pakistani counterpart, Asif Ali Zardari.
Relations between the US and Pakistan were severely strained for much of last year, reaching crisis levels following the killing of al-Qaeda leader Osama Bin Laden by US forces in Pakistan in May.