Lenin Moreno, of the governing left-wing Pais party, fell just short of the 40% needed to win outright on Sunday.
He will fight former banker Guillermo Lasso for the top job. There had been tension after long delays in the count.
National Electoral Council President Juan Pablo Pozo blamed the delays on "numerical inconsistencies" in 5.5% of the ballots.
In past elections, official results were announced on the same night as the vote but this time counting dragged on for four days.
Final results are still not in, but with only half a percent of votes left to count, Mr Moreno, 63, cannot possibly reach the 40% needed to stave off a second round.
With 99.5% of the votes counted he had won 39.3% of the votes, against 28.1% for Mr Lasso.
Lenin Moreno:
Guillermo Lasso:
The announcement that there would be a second round was celebrated by supporters of Mr Lasso, 61, gathered outside the National Electoral Council building.
Mr Lasso had earlier voiced concerns about the delay in counting saying it "did not smell right".
The conservative former banker says he is confident of winning the run-off with the backing of opposition candidates eliminated in the first round.
Third-placed Cynthia Viteri, who won more than 16% of the votes, has already called on her supporters to vote for Mr Lasso.
The election is being watched with interest in the region after other countries led by left-wing leaders, such as Argentina and Peru, have swung to the right in recent polls.
The winner will replace left-wing President Rafael Correa, who leaves office after a decade in power.

More than 3,600 firefighters are battling the King fire, 60 miles (97km) east of Sacramento.
The blaze has consumed wide swathes of timber in Eldorado National Forest and is only 5% contained.
"It's been an explosive couple of days," CalFire spokesman Daniel Berlant told the Associated Press news agency.
Widespread drought in the state has fuelled an active wildfire season.
As of early this week, California firefighters have battled more than 4,800 wildfires this year and were currently fighting 11 major fires, according to a local broadcaster.
Many of the people ordered to evacuate their homes were in Pollock Pines, 60 miles east of Sacramento.
Crews have been battling the fire for five days, but most of the losses have not been residences.
"We have had significant losses of public timber land, private timber land and watershed," Laurence Crabtree, a US Forest Service supervisor told the Sacramento Bee.
Further north, a blaze destroyed parts of the town of Weed, burning 110 homes and damaging 90.
High winds drove the fire quickly across town after it began on Monday. Two churches, a community centre and a library also burned to the ground.
Four firefighters lost their homes.
The Reverend Bill Hofer, pastor of Weed Berean Church, told the AP he was planning to return on Wednesday night - despite an evacuation order - to deter vandalism.
"The more people home with the lights on, the better," he said.
Ecuador's presidential election is set for a second round on 2 April, the electoral commission has announced.
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A central California wildfire threatening thousands of homes doubled in size overnight to 111 square miles (288 sq-km), authorities have said.