Georg Bätzing, bishop of Limburg, was nominated in a secret ballot during talks on the future of the Church in the western German city of Mainz.
The 58-year-old is faced with the complex task of modernising German Catholicism over the next six years, steering it through multiple crises.
Speaking about the issue of compensation for those people abused by members of the clergy, Bätzing said: "I hope we will be able to present an amicable solution at this meeting".
The four-day gathering concludes Thursday.
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Meanwhile the new chief must play a mediating role as the Church seeks to answer divisive questions on issues such as priestly celibacy and the role of women.
"I bring with me high esteem for other opinions -- for the authority and performance of the bishops, and for the views and participation of lay people, women and men," Bätzing told journalists.
Bätzing, ordained in 1987, has often expressed his support for the current synod and spoken about the need to restore the credibility of a Catholic Church neglected by its faithful and lacking priests.
Bishops in Germany are split between reformists and conservatives.
Reformers are willing to discuss subjects such as abolishing celibacy and women priests, while conservatives around the controversial Archbishop of Cologne Rainer Maria Woelki are opposed to such changes.
The synod is also followed very closely by the Vatican and would need its support for any reforms.
Pope Francis recently disappointed advocates of change by declining a request to allow married men to become priests in the Amazon.
In his response, the pope "perhaps did not take a stance on certain questions", according to Baetzing.
"That does not mean that we can't," he added.
Bätzing replaces Cardinal Reinhard Marx, also a liberal, who announced last month that he was retiring at the age of 66.
Elected bishop of Limburg, a town in western Germany, in 2006, he replaced the controversial Franz-Peter Tebartz-van Elst, who had resigned after being nicknamed the "bling-bling bishop" for his luxurious lifestyle and mismanagement.
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