A government statement said Prime Minister Alexis Tsipras had accepted his resignation.
In a tweet after a meeting between the pair, Mr Tsipras thanks Mr Toskas for his “courage” in stepping down.
Mr Tsipras added: “I warmly thank him for the honesty and dedication he displayed during the discharge of his duties.”
Mr Toskas offered to quit before, after the July 23 blaze in the small seaside town of Mati east of Athens.
But Mr Tsipras refused to accept his resignation.
The minister reiterated his desire to step aside again on Friday during a meeting with Tsipras, in a move that the main political opposition said came too late to appease the public.
Mr Toskas said in a statement: “This natural disaster, and the loss of so many people in Mati, overwhelms my desire to continue.
“This is something I had stated publicly from the first moment.”
Pressure has been growing on the government, which is trailing the conservative opposition in opinion polls.
It comes at a time when it had hoped to free Greece from years of bailouts prompted by its debt crisis.
There have been recriminations over what went wrong and led to the deaths of dozens in Mati.
Hundreds of people were trapped by towering walls of flames when they tried to flee.
Many jumped into the sea to survive but others died, either in their cars or when they were cornered on the edge of steep cliffs by the rapidly advancing inferno.
Last Friday Mr Tsipras said he took political responsibility for the deadly wildfire amid accusations that his government had failed to protect lives and to apologise for the disaster.
Seeking to deflect public anger, he told his ministers he was conflicted over whether the authorities had done everything right in response to the disaster.
The conservative New Democracy party said after the minister’s resignation: “Responsibilities have a name: Alexis Tsipras.
“He and his government do not have the courage to assume them 11 days after the tragedy.”
The greek premier’s office quickly responded and accused the conservative party of trying to score political gains from a national tragedy.
The death toll rose to 88 on Friday when a 35-year-old woman died from her injuries.
Her six-month old baby, the youngest victim, had died in her arms from smoke inhalation as they tried to escape the flames.
Greek authorities say they suspect the fire was set deliberately.
Arson is thought to be a frequent cause of forest fires in Greece, a crude method to clear the way for potential development.
Toskas’s duties have been assigned to Panos Skourletis, the country’s interior minister.