“Return trip is planned for Monday,” said the bishopric in the Bavarian city on its website, giving no further details.
Benedict's trip to Germany on Thursday was his first voyage out of Italy since his shock resignation in 2013.
The unexpected visit was made necessary by the deteriorating health of Benedict's 96-year-old brother Georg Ratzinger.
The only other time 93-year-old Benedict has left the Vatican since his resignation was a visit to the Castel Gandolfo papal palace outside Rome.
He was last in Germany in 2011.
Besides spending time with his brother, the pope emeritus also visited his parents' graves as well as the house he used to live in the district of Pentling.
Benedict, seen as a traditionalist in the Catholic Church, stunned the world when he became the first pope in 600 years to resign, citing health reasons.
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The former pontiff, whose original name is Joseph Ratzinger, now lives in a small former monastery inside the Vatican.
Benedict has largely stayed out of the public eye since standing down and being replaced by reformist Pope Francis.
His trip comes just days after numerous EU countries reopened their borders to Europeans as coronavirus lockdowns are eased.
Given his own frail health, Benedict was travelling with a doctor and a nurse, Vatican spokesman Matteo Bruni told reporters in Rome.
Both Benedict and his brother Georg were ordained priests on the same day in June 1951.
Georg Ratzinger went on to conduct the thousand-year-old Regensburg cathedral choir, known as the Regensburger Domspatzen.
But the renowned choir fell under the shadow of the Catholic Church's child abuse scandal after a 2017 report found that more than 500 choir boys suffered sexual or physical abuse at the institute from 1945 to the early 1990s.
The report criticised senior Church figures for failing to do enough to prevent the abuse, including Georg Ratzinger who led the choir from 1964 to 1994.
Ratzinger has said he knew nothing about the abuse and violence at the school.