He offered the Pope his resignation on his 75th birthday on 21 September, as required by canon law, according to a statement from the German-born cardinal to his diocese (Tuesday).
However, Francis has asked him to "remain at the head of the beloved archdiocese of Sao Paulo for another two years", said Scherer.
The cardinal, whose ancestors come from Saarland, has headed the diocese of Sao Paulo, which has more than five million Catholics, since 2007.
The Pope sometimes leaves the heads of important dioceses in office for some time beyond the episcopal retirement age if he values them.
At the 2013 conclave, many in the media gave the then 63-year-old Scherer a good chance of being elected the first pope from Latin America.
However, the choice fell in favour of his senior brother in office from Buenos Aires, Cardinal Jorge Mario Bergoglio (then 76), who has since led the Church as Pope Francis. Scherer is still one of the most influential churchmen in Latin America.