Officials say it sent notification of the result to the Government, which must still formally declare General Musharraf as the incoming president.
"We have informed the Government of the results of the October 6 presidential election and the winning candidate is General Pervez Musharraf," an election commission official said.
He says it is up to the Government's Cabinet office to formally give notice of General Musharraf's victory.
Once the announcement is made, it clears him to swear a new oath of office. He has pledged to do this as a civilian after resigning as army chief.
Becoming a civilian leader will meet a major demand of the international community, which has been outraged at his state of emergency.
Although General Musharraf won the October 6 elections, the Supreme Court put a block on officially declaring the result before it had a chance to rule on legal challenges to his candidacy.
General Musharraf, however, imposed emergency rule days before the court was due to rule, raising suspicion he feared it was going to go against him.
He then sacked Pakistan's chief justice and most of the Supreme Court's 16 other judges for refusing to swear a new oath of office.
Earlier this week the purged court - now stacked with loyalist judges - dismissed all the challenges and cleared the way for the election commission formally to notify the Government of his victory.
General Musharraf, who seized power in a coup in 1999, now has until December 1 to quit the army and swear himself in as a civilian.
His spokesman, Rashid Qureshi, says he cannot give a date when that will happen, but has promised it will not be long.
"Once the notification is issued there will be no delay on the president's side," he told AFP. © 2007 Australian Broadcasting Corporation