In his phone conversations with Karzai on Tuesday night and Wednesday, Kerry reiterated that the U.S. does not recognize the name "Islamic Emirate of Afghanistan," according to State Department spokeswoman Jen Psaki.
"The office must not be treated as or represent itself as an embassy or other office representing the Afghan Taliban as an emirate, government or sovereign," Psaki said.
"We were disappointed by the rollout on the ground, of course," Psaki said. "It was inconsistent with what we all believed the rollout would be."
In an attempt at damage control, Qatar's Foreign Ministry said late Wednesday that the Taliban had violated an agreement to call the office the "Political Bureau of the Taliban Afghan in Doha."
Psaki said Qatar has had the sign with the "Islamic Emirate of Afghanistan" name taken down.
Karzai does not always enjoy broad political support among Afghanistan's power brokers, but after seeing the Taliban open its new Doha office under its formal name and flag, many lined up behind him.
The Taliban gesture "is absolutely undermining the sovereignty of the country and its elected government," said Abdul Sattar Murad, a member of the powerful Jamiat-e Islami faction, whose leader, former Afghan President Burhanuddin Rabbani, was slain by a suicide bomber claiming to carry a Taliban peace message in 2011.
Murad said the hope among lawmakers was that Washington would also step in.
"It is now for the U.S. to find a way out of this," he told the AP. "I myself cannot say anything other than that the flag should be brought down and it should not be seen as a political representation of the so-called Islamic Emirate."
In his eight years as president, Karzai has often had rocky relations with his U.S. allies and has upset the Americans by questioning their motives. In June 2011, for example, he likened the Americans to occupiers, saying they were not in Afghanistan to help Afghans but "for their own purposes, for their own goals."
Some of Karzai's anti-American rhetoric in the past has appeared aimed at gaining political favor at home and staving off accusations he is a U.S. puppet, but in this case he does not appear to be posturing, said van Bijlert, who is with the Afghanistan Analyst Network.
"The opening of the office changed the place in the world of the Taliban," said van Bijlert. "It made them much more easily acceptable, it raised their profile, it makes them look respectable. And I think that just angered the Afghan government, that they had to take a backseat."
The Taliban ceremony also upstaged Tuesday's formal handover of all security operations in Afghanistan from U.S.-led forces to the Afghan army and police.
The international force is to be cut in half by the end of the year, and by the end of 2014 all combat troops are to leave and be replaced — contingent on Afghan governmental approval — by a smaller force that would be on hand for training and advising.
The U.S. has not yet said how many troops will remain in Afghanistan, but it is thought that it would be a force made up of about 9,000 Americans and 6,000 allies.
Shukria Barakzai, an independent member of parliament from Kabul, criticized Karzai's move to suspend negotiations with the U.S. on the security agreement, saying "we want to see our partners staying with us."
But she also questioned why the Taliban were able to open a political office in Qatar under their old flag.
"It's not really acceptable for the people of Afghanistan," she said.