“I now invite all Chinese Catholics to work towards reconciliation,” the pope wrote in a message to Roman Catholics in the world's most populous country.
Saturday's deal has paved the way for rapprochement between the Vatican and the Communist country, despite the fears of some in the persecuted underground Church.
“Some feel doubt and perplexity, while others sense themselves somehow abandoned by the Holy See,” the pope wrote.
“I am aware that this flurry of thoughts and opinions may have caused a certain confusion and prompted different reactions in the hearts of many.”
Shortly after the deal, Francis recognised seven clergy appointed by Beijing, which has not had ties with the Vatican since 1951.
On Wednesday he called on the bishops to publicly reunite with the Vatican.
“Regrettably, as we know, the recent history of the Catholic Church in China has been marked by deep and painful tensions, hurts and divisions, centred especially on the figure of the bishop,” he wrote.
“I ask them to express with concrete and visible gestures their restored unity with the Apostolic See.
'Wounds of the past'
There are an estimated 12 million Catholics in China, divided between a government-run association whose clergy are chosen by the Communist Party and the unofficial church which swears allegiance to the Vatican.
Pope Francis has sought to improve relations with China since he took office in 2013, but previous attempts foundered over Beijing's insistence that the Vatican give up recognition of Taiwan and promise not to interfere in domestic religious issues.
The Holy See is one of only 17 countries that recognise Taiwan, officially known as the Republic of China, instead of having diplomatic ties with Beijing.
“I hope that a new phase can be opened in China, which helps to heal the wounds of the past,” the pope wrote.
The agreement's aim is “to reestablish and preserve the full and visibleunity of the Catholic community in China.”
The deal was signed as churches have been destroyed in some Chinese regions in recent months, and there has been a clampdown on Bible sales.
Crosses have been removed from church tops, printed religious materials and holy items confiscated, and church-run kindergartens closed.
The Vatican cut ties with Beijing two years after the founding of the communist People's Republic.
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Some have warned that China could use the accord to further crack down on Catholic faithful, and Hong Kong's firebrand Cardinal Joseph Zen warned on Wednesday that the Vatican would abandon official ties with Taiwan.
Zen, the former Bishop of Hong Kong, is well-known for his vocal opposition to political suppression and his support for democratic reform.
“The Holy See, the Vatican, is ready to abandon Taiwan,” he told reporters in Hong Kong.
Taiwan officials say the Vatican has assured them the agreement will not affect diplomatic ties as Beijing makes a concerted effort to poach their dwindling allies.
Zen added the deal had also caused “spiritual suffering” in China's underground church.
“They fear that the Holy See is betraying the faith and that they want them to join this betrayal,” he said.
The Chinese Communist Party is officially atheist and religious groups are tightly controlled by the state.