Duterte said law enforcers have been ordered to frisk people entering cemeteries for deadly weapons and liquor and to "suppress noise."
Violators of the liquor ban will be fined P2,000 or meted a three months imprisonment.
Vendors have questioned the ban because it reportedly lacks an enabling law. But traffic management chief Celso Gempesaw announced last week they will stick to it citing a resolution and an ordinance approved in 1994.
The ordinance prohibits selling and drinking of liquors in both public and private cemeteries every November 1 and 2.
Duterte asked the public to suppress noise in cemeteries to "tolerable levels" to keep the occasion's solemn mood.
The mayor cited the change in the mode of remembering the dead through the years and appealed to the public for order.
"It used to be just a moment of meditation in prayer, now drinking is everywhere. Maintain a little discipline," he said, recalling the violence caused by drinking sprees and other festive ways of marking the occasion.
In 2002, playing loud music and dancing over tombs here on All Saints' and All Souls' Days were declared as violations of the public disturbance law.
Gempesaw earlier announced that violators of the Anti-Nuisance Ordinance will be "dealt with accordingly" .
He said traffic personnel will also be deployed in a 16-hour dispatch to ensure smooth flow of vehicles and pedestrians going in and out of cemeteries.
There are 11 public cemeteries in the city. These are located in Wireless, Ma-a, Mintal, Tugbok, Lubugan, Calinan, Panacan, Bunawan, Tibungco, Paquibato and Ulas.
There are at least five privately owned memorial parks.