Opposition parties that snubbed the vote claimed it was undemocratic and unconstitutional for the U.S.-backed general, who seized power in a 1999 coup, to run while still army chief.
The Supreme Court is weighing that argument before permitting the release of official results, though analysts question whether it would dare deny him victory and potentially throw the country into chaos.
In total, Musharraf won 671 votes, while the retired judge who was his main rival received just eight. Six ballots were invalid, election officials said. In all, 1,170 federal and provincial lawmakers were eligible to vote.
Musharraf dismissed criticism that the boycott had undermined the legitimacy of the election.
"Democracy means majority, whether there is opposition or no opposition," Musharraf, dressed casually in a gray jacket, told reporters on the lawn of his official residence. "A majority - a vast majority - have voted for me and therefore that result is the result."
Speculation persists that if Musharraf is blocked, he might declare martial law, and the army chief appeared annoyed when asked if he would step down as president if the Supreme Court ruled against him.
"Let the decision come and then we will decide," he said.
Musharraf's key international backer, the United States, gave an upbeat response on the conduct of the election, although the State Department stressed that the results were unofficial until the court verdict.
"Pakistan is an important partner and ally to the United States and we congratulate them for today's election. We look forward to the electoral commission's announcement and to working with all of Pakistan's leaders on important bilateral, regional and counterterrorism issues," Gordon Johndroe, a spokesman for the White House's National Security Council, said in Washington.
The ruling party celebrated Saturday's vote with fireworks and said it looked forward to parliamentary elections due by January, but their enthusiasm was not shared by a public cynical of Pakistan's elitist politics and the military's long domination of the country.
"We have a saying that 'He who owns the stick, owns the buffalo,"' said Ijaz Shah, a grocer relaxing on the lawns in front of the federal Parliament. "If the government really had support, there would have been thousands of people here to cheer it."
Musharraf's popularity has plummeted since a failed bid to oust the country's top judge in March and is struggling to contain a surge in Islamic militancy. He has promised to give up his powerful army post if he wins the election and restore civilian rule.
The Supreme Court ruled Friday that the official results can only be declared after it rules on complaints lodged by Musharraf's opponents on his eligibility. Hearings on those petitions will resume on Oct. 17. Musharraf's current presidential term expires Nov. 15.
Although the court this year has issued rulings that have shaken Musharraf's dominance, analysts doubted it would overturn the result.
"It will be extremely difficult for the Supreme Court to undo what has been done today, although that possibility remains," said Rasul Bakhsh Rais, professor of political science at Lahore University of Management Sciences.
"They will have to take into consideration the fact that a decision to annul the result would spin Pakistan into a serious political crisis."
Munir Malik, a lawyer for the main rival presidential candidate, Wajihuddin Ahmad, criticized the Election Commission's decision to count the vote and publish unofficial results.
"What they are trying to do is tell the Supreme Court 'Look, Pervez Musharraf has won an overwhelming majority.' So they are trying to intimidate the court," Malik said. "These judges have got to go with the people of Pakistan and not with the army generals."
It appears likely Musharraf will form an alliance with exiled Prime Minister Benazir Bhutto after the parliamentary elections - an alliance favored by the West to fight Islamic extremism. On Friday, he signed into law an amnesty quashing corruption charges against Bhutto, who is due to return to Pakistan on Oct. 18.
Bhutto's party abstained from Saturday's voting but did not resign from Parliament as other opposition factions did over Musharraf's candidacy.
The government hailed the vote as evidence of public support for Musharraf and a success for democracy in Pakistan. The opposition condemned it as a mockery, saying the presidential vote should have followed parliamentary elections.
Rather than seek a fresh mandate from the next parliament, Musharraf turned to the outgoing assemblies that had already authorized his current term. Critics say it is unfair as it means garnering 10 years in the presidency from lawmakers only elected for five.
"We will not accept him as president. He flouted the constitution, and he is a person who has hardly any respect for the rule of law," said Sadique ul-Farooq, an ally of former premier Nawaz Sharif, whose elected government was toppled by Musharraf eight years ago.
"Everything about the election was constitutional, legal, moral and legitimate," said Sher Afgan Khan Niazi, parliamentary affairs minister.
While there was minimal public response to an opposition call for a nationwide strike Saturday, dozens of lawyers clashed with police outside the provincial assembly in the northwestern city of Peshawar. They burned an armored police vehicle, threw rocks at officers, and burned an effigy of Musharraf before police swinging batons dispersed them.
Three lawyers and a policeman were injured, witnesses said.