Malesani named new Siena coach
Youth team coach Baroni took over from the dismissed Marco Giampaolo on October 29 but fans were upset with his low-key appointment and results did not improve.
"Siena announce they have reached an agreement with Alberto Malesani to be first team coach," a statement said.
Baroni stayed in charge for Sunday's 2-0 home defeat by fellow strugglers Atalanta despite the club openly courting former coach Mario Beretta but failing to reach a deal.
Malesani, who won the UEFA Cup with Parma in 1999, was last manager of Empoli in the top flight in 2008 before they were relegated.
Siena failed to strengthen in the close season and have just six points from 13 games and are six adrift of safety.
Coach sackings in Italian soccer have reached record levels this season and mid-table Palermo replaced Walter Zenga with Delio Rossi earlier on Monday.