The opposition, which has claimed Arroyo's camp manipulated the 10 May vote and cheated action film star Fernando Poe Jr of some two million ballots, fought the proceedings all the way and did not appear to be ready to give up.
Arroyo's victory margin was about one million votes. The military and police have been put on full alert for possible trouble.
The end of the count on Sunday paved the way for Arroyo's proclamation as winner by the full Congress. But the opposition can still question the committee's report later this week or file a protest, after the proclamation, to the Supreme Court election tribunal, a move that would likely take years to resolve.
Poe's people have also talked about a "people power" revolt like those that ousted dictator Ferdinand Marcos in 1986 and President Joseph Estrada, Poe's close friend, in 2001.
Arroyo took over midway through Estrada's six-year term and was seeking an electoral mandate to continue economic and other reforms in the poor southeast Asian nation that is one of Washington's closest allies.
The congressional committee worked through the weekend and finally finished counting the last of 176 provincial summaries of votes, called certificates of canvass, late on Sunday.
"The canvass is over. Arroyo has won"
Lawmakers and the audience broke into an applause, relieved that the acrimonious count was over. Some women approached legislators, handing them red roses. Opposition and the dominant pro-administration lawmakers shook hands.
"The canvass is over. Arroyo has won," Senate President Franklin Drilon said. "It was very difficult but this is democracy," he said, describing the infighting over the vote count as "harrowing".
The final tally had Arroyo with 12,905,808 votes and Poe with 11,782,232, a difference of 1,123,576 votes. Three other candidates were well behind.
Arroyo's vice presidential running mate, popular news anchor Noli de Castro, also won, according to the House-Senate committee tasked with counting the races for the country's top two offices.
Arroyo's spokesman, Ignacio Bunye, said earlier the president was preparing to lead street parties in the central province of Cebu, a vote-rich region, and gearing up for a 30 June inauguration.
Dozens have demonstrated
against the slow count
In recent weeks, opposition lawmakers and lawyers have alleged that several vote certificates appeared to have been altered to rob Poe of up to two million votes. They doggedly demanded that voluminous vote records from small villages be opened to ensure against fraud.
The dominant pro-Arroyo lawmakers consistently outvoted them, arguing that opening the vote records would delay the count and hamper Congress's ability to proclaim a winner before Arroyo's term expires on 30 June, which could spark political chaos.