People had watched in horror as 40 fire trucks rushed to the site and emergency workers set up a cordon around the cathedral, a jewel of French medieval Gothic architecture made famous by the paintings of impressionist Claude Monet in the 19th century.
The flames were officially put out at 4:30pm on Thursday (local time), local fire authorities said.
The spire had been in renovation for years and was surrounded by scaffolding and a white cover when the fire began about 120 metres above ground level.
Eye-witness Patrick Waeselynck told BFM television he was sitting at a cafe terrace when he heard shouts of "fire".
"I turn around and I see the cathedral spire, the tarpaulin which was protecting the restoration work, which was burning, big flames, black smoke," he said.
"The first thing we thought was what happened in Paris, it was a shock of course. But the police arrived, they set up a security perimeter, the firefighters arrived."
Workers involved in the renovation raised the alarm, fire brigade chief Stephane Gouezec said.
"The elements that were combusting when we arrived were plastic elements from the worksite," Gouezec told several TV channels just outside the building.
The Archbishop of Rouen Dominique Lebrun said he learned swiftly that no workers had been injured.
"I saw the flames, I saw the black smoke in particular, and then my fear was for the staff and for the site workers, that was my first concern, which was quickly reassured."
"I'm feeling a lot of emotions and a bit of confusion to be honest, because we carry out a lot of prevention exercises. We have many, many policies so that these accidents don't happen."
He added he thought a spark from a weld could have fallen onto a plastic cabin interior at the work site.
A local official said they were assessing if any parts of the cathedral or its art works had been damaged by the jets of water used to fight the fire.
"It is one of the most beautiful monuments in the city and we hope that there will not be too much damage," said Benjamin Gliksman, 42, who owns a record shop.
The 2019 fire at Notre-Dame in Paris also started during renovation works and destroyed the cathedral's roof, the spire and almost toppled the main bell towers.
Five years on, restoration of the Paris landmark continues and its reopening to worshippers is scheduled for December. As of April this year the renovation had cost 550 million euros ($NZ980 million).
Earlier this year a massive fire hit another historic European building, Copenhagen's Old Stock Exchange, toppling its spire. Large parts of the outer walls later collapsed.
