Filipe Luis was fired just hours after an 8-0 thrashing of Madureira in the regional Rio de Janeiro championship, called the Campeonato Carioca.
Portuguese boss Jardim resigned from his post at Belo Horizonte-based Cruzeiro in December after just 10 months in the job, saying that he needed to protect his "physical and mental health."
The 51-year-old has enjoyed a nomadic coaching career in Portugal, Greece, France, the Middle East and Brazil.
He guided Olympiacos to the Greek title in 2013 and repeated the feat with Monaco in France four years later, when he had a teenage Kylian Mbappe in his squad.
He has also won the Saudi and UAE league titles and the second division in his homeland.
"Welcome to Flamengo, Leonardo Jardim," the Rio de Janeiro-based club announced on their social media channels on Wednesday.
Jardim has signed a contract until December 2027.
Filipe Luis's sacking came just six months after he guided Flamengo to a fourth Copa Libertadores triumph and the Brazilian Serie A title.
"I leave in peace, with my head held high and with a clean conscience," Luis Filipe said in a goodbye post to Flamengo on his Instagram account.
The 40-year-old is a former Chelsea and Atletico Madrid defender.
He took over at Flamengo - Brazil's richest club - in September 2024 after he was promoted from their youth coach, a role he began following his playing retirement at the club in 2023.
But Flamengo suffered some disappointing results this year, losing the Brazilian Super Cup final to Corinthians and the Recopa Sudamericana to Argentina's Lanus after extra time in the second leg at the Maracana.