After Brazilian media speculated on the move, Jesus confirmed he would leave Rio after only 13 months and return to his native Portugal.
Benfica said Jesus had accepted their contract offer, in a statement on their website.
The 65-year-old, who won Brazil's first division title and the Copa Libertadores with Flamengo, had recently extended his contract until June 2021.
But the offer from Benfica was enticing due to the timing - in the middle of the coronavirus crisis in Brazil, which made the distance from his family more palpable, according to Globoesporte news.
Brazilian media reported Jesus would take up a three-year contract and earn 3 million euros (3.4 million dollars) per season. He trained the Portuguese capital's football club between 2009 and 2015 and won the Portuguese Primeira Liga championship three times with the team while he was at the helm.
