The out-of-contract 55-year-old, who arrived in Italy in 2013, will take charge of his final game when Napoli host Lazio on Sunday in effectively a playoff for the third Champions League spot in Serie A.
"This is the end of my two years experience here and I would like it to finish with a victory," said Benitez as he thanked the club, its president and its supporters.
Benitez, won the Champions League with Liverpool in 2005, the then UEFA Cup with Valencia in 2004 and the Europa League for Chelsea in 2013, is seen as one of the wiliest tacticians in world football.
Under his tenure Napoli were squeezed out of the 2014 Champions League at the group stage when they finished level on 12 points with Arsenal and Borussia Dortmund in the pool stage.
But they went on the win the Italian Cup and Supercup that year. The tough-talking coach suffered heavy criticism after defeat in the semi-finals of the Europa League two weeks ago to Ukraine outfit Dnipro, after also losing to Bilbao in the Champions League qualifying round in August.
"I thank 'Rafa' for these two seasons," said Napoli president Aurelio De Laurentiis. "He won me over when I met him two years ago in London and that first impression has since been confirmed."
Ruthless Real Madrid president Florentino Perez fired the latest incumbent of the Madrid hot-seat Carlo Ancelotti on Monday, and told the press his replacement would speak 'good Spanish'.
Ancelotti will be a hard act to follow as he delivered the club's most successful ever year in 2014, with the Copa del Rey, UEFA Super Cup and Club World Cup adding to the glory of ending a 12-year wait for their tenth European Cup.
Benitez has won three European trophies but there are plenty of doubters as to whether he is the right man to deliver on the expectations of the world's most expensively assembled squad.
When Benitez took over then Champions League winners Inter Milan in 2010 his reputation took quite a battering despite winning the Club World Cup, he never won over the dressing room and was fired in late December of his first season there.
However, arguably his best work came during his last job in Spain over a decade ago in winning two league titles and the UEFA Cup with Valencia.