The 56-year-old enjoyed a successful reign with the Argentine giants, winning the league title and Copa Argentina, as well reaching the Copa Libertadores final.
But opposition from Boca supporters was enough for president Daniel Angelici to decide against a contract extension.
"After a conversation I had with Julio Cesar Falcioni, we decided that we will not renew his contract because after what happened on Saturday it would be difficult to work under that pressure," Angelici told reporters.
"Last Saturday the Bombonera (Boca fan section) spoke and we understood that it was better not to renew Falcioni's deal."
Angelici also responded to accusations that supporters had turned against Falcioni as a result of negative comments towards the coach by former favourite Juan Roman Riquelme.
"It was probably just newspaper talk that Riquelme prejudiced the crowd against Falcioni," he added.