Dozens of people were caught up in the huge blast on Rue de Treviso in the ninth district of the French capital just before 9am local time.
A Spanish tourist, who was reportedly visiting the French capital with her husband and staying in a hotel opposite the bakery, died in hospital.
Spain's Foreign Minister Josep Borrell tweeted: "I deeply regret the death of three people after the explosion in central Paris, including a Spanish woman."
He shared condolences to her relatives and "wishes for a quick recovery to the other injured Spaniard."
The French interior minister Christophe Castaner initially said four people had been killed but the Paris prosecutor later corrected it to two.
At least nine people are fighting for life, and 37 are in less serious conditions, they confirmed.
Many still in their pyjamas had to be rescued from their windows as flames continued to rage in the Hubert bakery, which sells breakfast cakes and pastries.
Neighbours say they smelt gas first thing on Saturday morning, before calling the emergency services.
A spokesperson for the fire service said crews were already at the scene when the explosion happened and that investigations are ongoing to determine the exact cause of the blast.
Mr Castaner said a "pocket of gas" had built up in the building and emergency services were called to investigate at 8.37am local time on Saturday.
He added: "When they were there, a massive explosion happened. One of the fire fighters remained under the rubble for two and half hours.
"There are other very serious casualties. The area has been secured as the fires are put out."
Paris Mayor Anne Hidalgo, who was also at the scene, extended a "message of affection and solidarity" to the victims.
Witnesses described waking up to the "carnage" as the blast gutted buildings, blowing out the windows and flipping cars on the street below.
Shocking pictures from the scene showed the devastation as the entire street was strewn with rubble and shattered glass.
Customers having breakfast in a hotel restaurant opposite are believed to be among the victims after being "knocked unconscious" in the blast.
Hotel worker Pedro, who suffered head injuries, told RT France: "I heard a big explosion… a lot of things fell. Rubble, the roof – I just had time to bend down and cover my head."
An eyewitness who was staying at a hotel nearby said he saw saw a huge fire erupt in the building blown out by the blast.
David Bangura, 38, said: "There was broken glass everywhere, storefronts were blown out and windows were shattered up to the third and fourth floors."
He said that as he approached the scene, a woman was crying for help from the first floor of a building: "Help us, help us, we have a child".
One girl told RT France: "We were all sleeping and there is a noise, we thought it was an earthquake."
Another woman, who lives above the bakery, told the news website: "All the windows of the apartment exploded, all the doors that were open came out of their hinges.
"To get out of the room I had to walk on the door, the children were panicked, they could not get out of their room."
One woman who lives nearby said she had "nothing left" of her flat after the explosion destroyed her home.
A police spokesperson, who didn't want to be named, said: "A whole shop front has been taken out, and other buildings have also been severely damaged.
"It’s a Saturday morning – a lot of people were at home."
Pictures showed fire crews evacuating residents trapped in the apartments above the shop and inspecting adjoining courtyards.
Three emergency helicopters were used to take victims to hospital, after landing by the Garnier Opera House.
Debris from a burned car and broken glass littered the pavement, while a vehicle from gas company GRDF was stationed nearby.
The building is around the corner from the Folies-Bergere theater and not far from the shopping district that includes the famed headquarters of Galeries Lafayette.
Interior Minister Christophe Castaner, who was at the scene, said "the situation is under control" but warned the explosion had caused a "heavy toll.
An investigation was opened, according to the Paris prosecutor's office, which would not comment on what possible causes were being investigated.
It came amid heavy security in Paris and around France for protests expected later Saturday.
Thousands of police will take to the streets for an Act 9 "Day of Rage" by the anti-government Yellow Vest movement.
They have been behind numerous acts of vandalism, including destroying parts of the Arc de Triomphe itself.
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