Estrada won the presidential race in 1998, beating Alfredo Siojo Lim, a former police chief and who until this week's local and senatorial elections was serving his fourth term as mayor of Manila.
After losing the 1998 presidential race, Lim, 83, ended up in Estrada's Cabinet until the 76-year-old former film star president was overthrown and jailed in 2001. He was found guilty of plunder in 2007 and sentenced to life in prison.
But only months later, Estrada was freed through a pardon by President Gloria Macapagal Arroyo, who had replaced him, and he began his political comeback, albeit successful only at the local level.
He ran for president in the 2010 but came in second to Sen. Benigno Aquino III.
Estrada traded many barbs with Lim on the campaign trail before this week's vote, a report by The Philippine Star newspaper said.
Election officials said around 76 percent of eligible voters cast ballots in what Philippine National Police called a campaign season more peaceful than many others in recent years.
However, there was a series of ambushes and explosions during the weekend that left at least two people dead, the Star reported earlier. Also, the nephew of a mayoralty candidate in South Upi was killed in an ambush and a police officer was killed in Borongan.
Estrada's win was all but official after the latest tally by the Commission on Elections showed him with 338,004 votes to Lim's 304,595, with 5 percent of precincts to come in, the Star report said.
Estrada didn't wait for an official announcement before releasing a statement thanking the people of Manila for showing faith in him.
He thanked "the great people of Manila for putting a true son of Manila at the helm of the Philippine capital city," a report by GMA News Online said.
He asked his "worthy political opponents and the entire 1.6 million people in Manila to finally leave politics behind and to rally behind me in putting Manila back on the pedestal of being one of the greatest cities of the world, the Paris of Asia."
Estrada's election shows the former successful film actor -- he played the lead role in one move about a 1950s Filipino mob boss -- still can draw crowds despite a shady past in real life, a report by the BBC said.
Allegations of involvement in corruption and illegal business transactions played into the hands of his political opponents while he was president and he was impeached and tried by the Senate.
When the trial collapsed, after some prosecution evidence was ruled inadmissible, anger protesters filled the streets.
He was ousted in a popular revolt backed by the Catholic Church and the army in January 2001, the BBC said.
He was sentenced to life in prison after being found guilty of plundering state funds and accepting millions of dollars from illegal gambling syndicates.