Ms Liu's departure was "wonderful news" but harassment of her family remained a risk to her freedom to criticise China, Amnesty International's China researcher Patrick Poon said.
During an earlier stop-over in Helsinki, Finland, she was seen spreading her arms and grinning widely.
Li said that China will cooperate with Germany "in the spirit of mutual respect, equality, mutual understanding and accommodation as well as fair competition to better achieve win-win results", according to China's foreign ministry.
Her late husband, Liu Xiaobo, died of cancer in July 2017 after spending more than eight years in prison for his advocacy of human rights in China.
China has been seeking to bolster its ties with the European Union amid a trade war with the United States.
The authorities' refusal to allow Liu Xiaobo or Liu Xia to leave China at that point prompted an worldwide outcry.
Specifically, both sides plan to strengthen cooperation on digitization, autonomous driving, artificial intelligence, new energy vehicles, and scientific and technological innovation - the items that the USA government aims to hit the hardest via its trade war, which targets advanced technologies that are the focus of the "Made in China 2025" plan.
He died last summer of late-term liver cancer after the Chinese government repeatedly denied his request to receive medical treatment overseas.
Hua Chunying, a Chinese foreign ministry spokeswoman, said Liu's travel to Germany for medical treatment was "of her own free will".
In April, Liu Xia said she was "prepared to die" under house arrest, during a telephone conversation with her friend Liao Yiwu, an exiled writer.
Guards ate and slept outside her door, driving away well-wishers, activists, journalists and diplomats - a slow-burning ordeal worse than death, she said in a rare recording that emerged in May.
Chinese authorities put Liu under house arrest in 2010, days after the Norwegian Nobel Committee awarded her imprisoned husband, Liu Xiaobo, the Peace Prize, infuriating the Chinese government.
"In the last two years, our parents and her husband died one by one", Liu Hui said. Her release is a testament to the power of collective voices being raised in support of those who others would brutalize into silence. Liu Xiaobo was guilty of drafting the Charter 08 manifesto (read in full), which calls for democracy, freedom of expression, and human rights in China. "I am very excited when my sister left safely", he said.
Liu's departure comes a day after Chinese premier Li Keqiang met German Chancellor Angela Merkel in Berlin.
Liu Xia poses with a photo of her and her husband during an interview at her home in Beijing on December 6, 2012.
And Sophie Richardson, China director of the New York-based Human Rights Watch (HRW), expressed "relief" at the news.
"While precise details of Liu's flight out of China are unknown, the only Finnair flight that left Beijing Capital International Airport bound for Berlin on Tuesday morning was Flight AY86, which took off at 10.55am, according to the airport's website".
Germany, which is also home to dissident artist Ai Weiwei, has been outspoken on rights in China.
Liu Xia, the wife of Chinese dissident Liu Xiaobo, talks to the media in Beijing February 11, 2010. Liu declined to give a formal interview, citing fears for her younger brother.
While news and information about the couple are strictly censored in mainland China, people in Hong Kong took to Facebook to send their good wishes to Liu Xia.
Liu Hui said it felt like he was able to finally unload the "dead weight" off his shoulders.
"Liu Xia might not be able to speak much for fear of her brother's safety", Poon said.
Diplomats have said that authorities continued to monitor Liu Xia after the death of her husband and she had only been able to meet and speak to friends and family in pre-arranged phone calls and visits.