Gonzalez told supporters she does not accept the results and will demand a recount, calling it "the worst and most grotesque electoral fraud in the history of Ecuador".Â
With nearly 93 per cent of ballot boxes counted, Noboa had 55.8 per cent of votes, compared to Gonzalez's 44.1 per cent, a difference of more than one million votes.
The results were a sharp contrast to the February first round, where Noboa finished just 16,746 votes ahead of Gonzalez.
"We inform the Ecuadorean people that with more than 90 per cent of the ballot boxes processed nationally there is an irreversible trend in the second round of voting," Diana Atamaint, the head of the national electoral council said in a statement to the press.
"The winning duo is Daniel Noboa Azin and (vice president-elect) Maria Jose Pinto."
Gonzalez expressed disbelief over the results to chanting supporters in Quito.
"I refuse to believe that a people would prefer lies instead of truth, violence instead of peace and unity," Gonzalez said.
"We are going to demand a recount and for them to open ballot boxes."
The candidates and Gonzalez's mentor, former President Rafael Correa, had urged some 90,000 polling-place observers to guard against electoral fraud.
Correa said on social media the results were "impossible".