Zanetti's side have failed to score so far this season and conceded 12 goals. The 40-year-old former Empoli player was appointed at the start of last term and they finished 14th.
Before taking charge at Empoli, he won promotion to Serie A with Venezia but was sacked in April 2022 after a run of eight defeats left them bottom and they ended up being relegated.
Zanetti took over at Empoli from Andreazzoli, who now returns for a fourth spell as manager having steered them to promotion to Serie A in 2018 before relegation a year later. He returned for the 2021/22 season and helped keep them in Serie A.
The 69-year-old was most recently in charge of Serie B club Ternana where took over in December 2022 but resigned after they took 12 points in 12 games. He was reappointed by the club in June but rescinded his contract before the season began.
Empoli next host Serie A leaders Inter Milan on Sunday.
