The commission reported on Monday that Saied, who hasn't held elected office before, received more than 70% of the vote.
His opponent, media mogul Nabil Karoui, got just over 27%.
The results confirm exit polls from Sunday's election.
Nabil Bafoun, head of the electoral commission, said "by looking at the result ... and knowing that it represents an absolute majority for this second round of the presidential elections, we, the Tunisian electoral commission, declare Mr Kais Saied winner of the presidential elections."
The commission said that Saied got a majority of the votes in each of the 33 electoral districts.
He exceeded 90% in six traditionally very conservative southern districts.
The 61-year-old Saied is an independent outsider but has support from moderate Islamist party Ennahdha, which won Tunisia's parliamentary election last week.
He has promised to overhaul the country's governing structure to give more power to young people and local governments.
Karoui, 56, told supporters Sunday the race wasn't over because his legal team would explore options.
He was arrested on August 23 in a corruption investigation and released with only two days left to campaign.
If no legal action is taken to challenge the results, the electoral body is set to announce the definitive vote count on Thursday.
Tunisia's parliament will then hold an extraordinary session during which the newly elected president will be sworn in and will formally start his five-year term.
The presidential vote was held early following the July death in office of President Beji Caid Essebsi.
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