U.S. officials also said Wednesday that it was Chen who decided to go to the hospital in Beijing for treatment.
"He did so on the basis of a number of understandings. China acknowledged that Mr. Chen will be treated humanely while he remains in China," a senior U.S. official said.
Chen, who was reunited with his wife and two children at the hospital, is to have access to U.S. doctors and other visitors, the official said.
"They will remain together with him as a family," the official said. "He had not seen his son in a few years, and his wife had not seen him either, so this was a family reunification after a long and difficult separation."
Clinton was the first person to call Chen after he left the embassy, a U.S. official said. Chen said to Clinton, in broken English, "I want to kiss you," the official said.
Clinton said she was pleased that U.S. officials "were able to facilitate" Chen's "stay and departure from the U.S. Embassy in a way that reflected his choices and our values."
"I was glad to have the chance to speak with him today and to congratulate him on being reunited with his wife and children," she said in a written statement.
On Thursday, in a speech to Chinese officials, she referred to human rights without mentioning Chen. "Now, of course, as part of our dialogue, the United States raises the importance of human rights and fundamental freedoms because we believe that all governments do have to answer to citizens' aspirations for dignity and the rule of law and that no nation can or should deny those rights," she said.
Douglas Paal, a China analyst at the Carnegie Endowment for International Peace, said Chen's reversal may be a way to put Beijing on notice "that the whole world is watching you, and you'd better follow through on your promise and more."
"The Chinese are now under an open and transparent obligation to provide this guy the security and assurances they told the Americans they would. Otherwise, their relations with the United States will take a sharp downturn," said Paal, a former State Department and CIA official.
Last month, Chen evaded guards who had kept him under house arrest for more than 18 months in Shandong.
He was confined to his home after serving four years in prison, apparently over his legal advocacy for what he called victims of abusive practices such as forced abortions and sterilizations by China's family planning officials.
The activist made his way to Beijing on April 22, moving between safe houses before seeking refuge in the U.S. Embassy. Friends and fellow activists had raised concerns about his health.
Chinese officials had guaranteed that no further legal issues will be directed at Chen and that reports of mistreatment against him will be investigated, a U.S. official said Wednesday, before Chen's change of heart.
He had said he wanted to stay in China and so was to have been moved to a "safe environment" away from the province where he was kept under house arrest, another U.S. official said.
Chen "may attend a university to pursue a course of study," the official said.
"Mr. Chen has a number of understandings with the Chinese government about his future, including the opportunity to pursue higher education in a safe environment. Making these commitments a reality is the next crucial task," Clinton said.
"The United States government and the American people are committed to remaining engaged with Mr. Chen and his family in the days, weeks and years ahead."
The State Department's Nuland said U.S. officials didn't speak to Chen "about physical or legal threats to his wife and children," and Chinese officials didn't "make any such threats to us."
"U.S. interlocutors did make clear that if Chen elected to stay in the embassy, Chinese officials had indicated to us that his family would be returned to Shandong, and they would lose their opportunity to negotiate for reunification," she said.
China demanded an apology from the United States for its handling of the situation.
Liu Weimin, a spokesman for the Chinese Foreign Ministry, in comments reported by the state-run news agency Xinhua, called the U.S. activity "interference in Chinese domestic affairs, and this is totally unacceptable to China." He said Chen had left the embassy "of his own volition."