In suspending aid, the United States is showing it will no longer give the benefit of the doubt to Pakistan's military after a long debate on how to handle the powerful institution.
President Barack Obama's administration took office with a determination to strengthen Pakistan's weak democratic leaders and crafted a civilian aid package accordingly, all the while trying to nurture ties to a suspicious army.
But now the administration has taken a major -- and, in some analysts' view, risky -- step of deferring $800 million for the army and saying it will not resume full funding without what it sees as progress on fighting insurgents.
"There has been growing estrangement but this represents a real change of gears because up until now the thrust of our relationship has been our militaries working together, whatever else happens," said Marvin Weinbaum, scholar-in-residence at the Middle East Institute.
"This is a high-stakes gamble in a way -- that somehow this is going to get the military to wake up to the fact that their long dependence on the United States, for equipment in particular, could end," he said.
Pakistan's military, used to commanding respect at home, was chastened by its failure to detect a top-secret US raid in May that killed the world's most wanted man Osama bin Laden a short distance from the country's top academy.
The Obama administration, if not much of the US general public, was restrained in its public comments after the raid, believing that the United States had little to gain by risking its access to the war partner.
But some US policymakers and analysts were distraught at what they saw as a bellicose reaction from Pakistan since the bin Laden operation, including ordering out up to 200 trainers in the country.
"The US realized that maybe this isn't just about the Pakistanis' capability, maybe there is also a will issue," said Lisa Curtis, a senior research fellow at the conservative Heritage Foundation.
"This is a strong signal that the US is no longer satisfied with Pakistani cooperation and more willing in the aftermath of bin Laden's death to follow through," she said.
Admiral Mike Mullen, the top US military officer, has publicly supported ties with Pakistan's army and has tried to maintain a cordial relationship with his counterpart, General Ashfaq Kayani.
But Mullen voiced alarm last week after concluding that Pakistani intelligence killed journalist Saleem Shahzad, whose body was found last month bearing marks of torture after he wrote of links between rogue elements of the military and Al-Qaeda.
US officials have also voiced concerns about Pakistani official elements' dealings with Afghanistan's Taliban and anti-Indian Islamic militants. Secretary of State Hillary Clinton will visit New Delhi next week.
Much of the deferred aid involved funding for the trainers. The United States planned an annual $2.7 billion to Pakistan in security assistance, meaning that most military aid -- and all civilian aid -- will proceed.
Pakistan's army has so far brushed aside the move, saying that it has resources to fight on its own.
But tensions could soar if Pakistan threatens to close the crossing for war supplies headed into Afghanistan, a step Islamabad took briefly last year which would throw into question the US rationale for the partnership.
Shuja Nawaz, director of the South Asia Center at the Atlantic Council, said that Pakistan has not threatened any drastic steps and that the army's actions were partly driven by hopes of shoring up public support.
For Pakistan, the latest tensions date from before bin Laden's killing to the case of Raymond Davis, a CIA contractor who shot dead two Pakistanis on a street. He was freed after payments to the victims' families.
Nawaz said Pakistan's military knew that a worsening relationship was not in the country's interest as it could spiral downward and hurt other priorities -- such as US support for Pakistan in international financial institutions.
"I think there is a desire to maintain the relationship. There is a question of finding the way to achieving that objective," he said.