The death toll rose to three later Saturday, per the French and Spanish governments, after earlier being mistakenly put at four.
French Interior Minister Christopher Castaner had admitted to the mistake after being corrected by police, a police spokeswoman said.
Ten people were seriously injured, while 37 received minor injuries.
The explosion took place around 9 am (0800 GMT) on Rue de Trevise, not far from the Paris Opera, at the same time as the city was bracing for the ninth weekend of Yellow Vest protests.
The cause of the blast is still unclear, though authorities suspect a gas leak to be behind it. "At this point, we can say that it is apparently an accident," Paris prosecutor Remy Heitz said on broadcaster France Info.
The fire department had been called due to a gas leak in the bakery, a police spokeswoman told dpa earlier Saturday.
Around 100 police officers and 200 firefighters were deployed to the scene, according to the interior minister.
At the scene, the windows of nearly all the surrounding buildings are blown out, while cars on the street have broken windscreens. The remains of the bakery that once stood there can barely be discerned.