Mr Monguillot was attacked after he reportedly asked three passengers to wear face coverings – mandatory on public transport in France during the coronavirus pandemic – and to see their tickets.
Two other men have been charged with not assisting a person in danger, while a fifth man faces a charge of attempting to hide a suspect.
Thousands of people dressed in white to took part in a march honouring Mr Monguillot in Bayonne on Wednesday.
A French bus driver has died after being attacked by passengers during an alleged row over masks.
Philippe Monguillot, 59, died in hospital on Friday, five days after he was left brain dead by the assault in Bayonne, in southwest France.
His daughter, Marie, said his family and doctors had made the decision to “let him go”, Agence France-Presse reported
The city’s mayor Jean-Rene Etchegaray, condemned the “barbaric” attack.
He tweeted: “Philippe Monguillot has left us. He succumbs to barbaric aggression in the exercise of his profession.
“A faithful servant of the public service, he leaves the image of a generous man. Support for colleagues in grief. Our affection for his grieving wife and family.”
French prime minister Jean Castex said Mr Monguillot’s death following the “cowardly assault” while he was trying to do his job “touches us in the heart”.
Thousands of people participate in a march as a tribute to French bus driver Philippe Monguillot in Bayonne, southwestern France, 8 July 2020. (Caroline Blumberg/EPA)
He tweeted: “The Republic recognises in him an exemplary citizen and will not forget him. Justice will punish the perpetrators of this abject crime.”
Interior minister Gerard Darmanin sent his condolences to Mr Monguillot’s family, saying those involved in the incident must be punished.
He tweeted: “I extend my sincere condolences to the family, relatives and colleagues of Philippe Monguillot, bus driver who was violently attacked last Sunday in Bayonne.
“This heinous and cowardly act must not go unpunished.”
He added: “I will go tomorrow to #Bayonne to take stock of safety in the city with the heads of state services and meet the drivers and unions of public transport.”
The European Transport Workers’ Federation said it was “shocked and saddened to learn of the senseless and heinous assault”.
The union called for greater protection for workers in the industry, saying in a statement: “For us, it is essential that management quickly implement measures to ensure the safety of drivers.
“Companies must value lives over profits.”
It added on Twitter: “We express our support and solidarity with Philippe Monguillot’s family, friends and colleagues.
“We condemn this barbaric and senseless act, and once again, we demand the swift implementation measures to protect workers from such attacks!”