The phone diplomacy occurred after Karzai said the Afghan government had suspended security talks with the United States in Kabul "in view of the contradiction between acts and the statements made by the United States of America in regard to the peace process."
"The secretary spoke with President Karzai last night and again this morning," State Department spokeswoman Jen Psaki told reporters at a daily briefing in Washington.
"The secretary reiterated the fact that we do not recognize the name Islamic Emirate of Afghanistan. ... He noted that the government of Qatar has taken steps today to ensure that the political office is in compliance with the conditions established by the government of Qatar for its operations, and noted also that we are pleased that the Qatari Ministry of Foreign Affairs has issued a statement clarifying that the name of the office is the Political Office of the Afghan Taliban and not the Political Office of the Islamic Emirate of Afghanistan and has had the sign with the incorrect name in front of the door taken down."
She added the Taliban 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 the Obama administration remains committed to "peace and reconciliation" in a "democratic and unified Afghanistan."
Despite Karzai's announcement the talks with the United States were suspended, Psaki said the administration is still "committed to continuing these negotiations and open to discussing, and are hopeful that we will be able to do that."
She later said President Obama said while in Germany Wednesday that "we always knew that there would be bumps in the road."
"This is a case where there have been decades of strife. They are at war and continue to be at war," she said. "Clearly, this is challenging. But diplomacy is hard, and we are -- remain focused on it. Obviously, as evidence of that ... are the secretary's calls, the statements the president has made, and our continued commitment to moving towards a political reconciliation."
A Karzai spokesman told the BBC the president objected to the title of the Taliban office in Doha, Qatar, as well as the Taliban flag flying over the new facility.
"We oppose the title the 'Islamic Emirate of Afghanistan' because such a thing doesn't exist," Aimal Faizi said. "The U.S. was aware of the president's stance."
Karzai's announcement Wednesday came the day after the Taliban's opening of the Doha office.
American officials had said they expected U.S.-Taliban talks to begin soon, followed by contacts between the Taliban and Karzai's peace envoys.
Security discussions between the United States and Afghanistan concerned a post-2014 mission that would provide for a limited number of military trainers and counter-terrorism forces to remain in Afghanistan once the coalition's mission ends.
Karzai's announcement comes a day after NATO turned over the security responsibilities for the country to the Afghan government.
Failure to reach a similar agreement in Iraq led to the complete withdrawal of U.S. forces at the end of 2011.