"Maradona is no longer the Gimnasia coach," club president Gabriel Pellegrino said on Argentina's Radio La Red.
"He said he was here to add to things, not to divide," was Pellegrino's explanation for the World Cup-winner's decision.
Reports in Argentina suggested Maradona's departure was linked to an imminent management shake-up at the club in La Plata, 50 kilometres from Buenos Aires.
Maradona was no longer keen on remaining at the club after Pellegrino, the man who brought him back to Argentine football, pulled out of running for re-election as the side's president next Saturday.
Before his last match in charge, he tied his future to Pellegrino's: "I talked to the president and told him that I would continue if he continues."
The 59-year-old former Argentina captain and coach took over at Gimnasia in early September, when it was bottom of the 24-club Superliga.