The Giallorossi were humbled by Cagliari on Friday, and the Czech trainer was relieved of his duties on Saturday following the 4-2 defeat, and a fans' protest after the game.
Aurelio Andreazzoli will now take over the first team responsibilities with Baldini insisting they had no alternative solution to the sacking of Zeman.
"We decided to remove the coach from his position," Baldini said.
"It was the only decision we could make. We evaluated the situation and have given the team to Aurelio Andreazzoli who has our faith.
"Knowing the players, this is the best decision to make at this moment. We spoke to all the management staff and the club owners gave me this responsibility."
Director Sabatini added: "I am very upset at this situation, the season does not end like this. Zeman was unlucky, but you will see the story doesn't end this way."
Laurent Blanc has already reportedly turned down taking the job as the club looks for a replacement. The Giallorossi sit in eight position, nine points off the Champions League places.