The club sit second bottom of the top flight, having won just two of their opening 12 games this season.
After a glittering playing career with the likes of Real Madrid and Chelsea, Makelele spent time as a coach at Paris Saint-Germain before taking his first managerial post at Bastia at the end of last season.
However, after less than six months in charge, Bastia are now on the hunt for a new head coach after confirming the former France midfielder's departure on Monday.
"The directors' committee of SCB informs all of its supporters and partners that from this day, Claude Makelele is no longer the head coach of SC Bastia," read a statement on the club's official website.
"As of this afternoon, training will be handled by Ghislain Printant and Herve Sekli until the appointment of the next head coach."
Makelele's final game in charge of Bastia came on Saturday, when Sambou Yatabare's goal gave Guingamp a 1-0 win at the Stade du Roudourou.
