Montella, who coached Fiorentina between 2012 and 2015, returned to the Artemio Franchi in April, replacing Stefano Pioli.
But he failed to win any of his eight games in charge at the end of 2018-19, seemingly casting his future in doubt.
However, it has now been confirmed that Montella will take charge of the Viola next season, following a meeting with Commisso on Friday.
"I'm very happy. I met Rocco Commisso for the first time in person and his enthusiasm exceeded all my expectations," Montella told Fiorentina's official website.
"He conveys a lot of positivity and I'm sure this feeling will spread through to everyone, the team and the fans.
"Now I can't wait to not only start the season but also get to work and try to give the new owners and Fiorentina fans the satisfaction they deserve."
The 44-year-old Montella returned to Fiorentina after spending nearly a year out of the game, following his sacking at Sevilla in 2018.
But he was defeated in the quarter-final of the Champions League by Bayern, heavily defeated by Barcelona in the Copa del Rey final and finished his tenure at Sevilla with a nine-game winless run in the league, leading to his dismissal.
Prior to Sevilla, Montella spent parts of two seasons in charge of Milan. A successful first season at the club, which saw him lead Milan to a sixth place finish, was followed by a disappointing start to the 2017-18 campaign. As a result, Montella was replaced in November 2017 by Gennaro Gattuso.
He had worked at Sampdoria prior to heading to Milan, after his initial stint at Fiorentina.
Montella will now look to build upon his end of season run at Fiorentina, which saw his side fail to win a single game in any competition after February 17, and ultimately finished 16th, just three points clear of the relegation places.