Investigators were still examining about 100 ballot boxes to clear up lingering fraud allegations, but the election's chief technical officer said the count was effectively "over and done."
"It's just these last dribs and drabs to be approved," David Avery told The Associated Press. "It's really nothing that can affect the outcome."
Election officials have said they will not announce official results of the Oct. 9 vote until investigations of irregularities alleged by Karzai's main rivals have been concluded, which could take until the weekend. The winner's inauguration is to take place about one month later.
The official election Web site had yet to add in all the latest results, still listing the count as 98.4 percent complete as of Tuesday afternoon. Karzai had 55.5 percent of the votes, 39 points ahead of his closest rival, former Education Minister Yunus Qanooni.
Karzai, installed as interim president after the fall of the Taliban in 2001, needed more than 50 percent to avoid a run-off and secure a five-year term in which he has pledged to raise living standards after a quarter-century of fighting.
Earlier Tuesday, presidential spokesman Jawed Ludin said Karzai had been clicking enthusiastically on the colorful election Web site to monitor his progress.
"He is happy and satisfied" with his lead, Ludin said. "God willing, he will hold onto it."
Karzai has racked up more than 90 percent support in many parts of the south and east, which is dominated by his fellow Pashtun tribesmen, and leads in all Afghanistan's major cities.
But rivals have eclipsed him across much of the north and center, the heartlands of Afghanistan's ethnic minorities, and charge that Karzai is only ahead through cheating.
Investigators had held back hundreds of boxes, and say they have clear evidence of ballot-stuffing in some cases, though not on a scale that could overturn Karzai's majority.
"Some boxes were so obviously stuffed that we don't believe they were legitimately cast votes," Ray Kennedy, the deputy chairman of the commission, told The Associated Press.
That remark was an indication that the election board will acknowledge irregularities — the key condition set by Karzai's closest rival for conceding defeat.
"If the fraud was not so serious, we would accept that Karzai has won," Qanooni's running mate, Taj Mohammed Wardak, told AP.
"I hope there was not so much fraud so our democracy is safe. If it was serious, then we are sad and it will affect the election result. We will accept the conclusion of the panel."
Avery said all but about 100 of the ballot boxes were released on Tuesday after inspectors found no evidence of foul play. Officials were expected to complete their inspection of the remaining boxes by Thursday.
Still, election managers say they will reserve overall judgment on whether the election was "free and fair" until they issue their final report.
While irregularities detected during the counting process are under examination by the electoral board's legal experts, a panel of foreign election specialists is looking separately into problems on polling day.
The three-member panel was established after Qanooni and 14 other candidates threatened to boycott the poll because of a mix-up with ink used to mark people's fingers to prevent multiple voting.
By Stephen Graham