Authorities in the southern port city said the body of one man had been retrieved in the rubble on Tuesday after an overnight search.
The body of a woman was found later in the day and a third body found shortly afterwards.
Officials warned there were probably other casualties after the two adjoining buildings disintegrated, blocking the street with massive piles of rubble.
Ten skips-full of rubble had been removed in the search for more victims by Tuesday morning.
Two passersby were reported lightly injured when the incident occurred around 9.00am (0800 GMT) near the bustling Old Port and waterfront.
The authorities had evacuated several dozen residents from neighbouring buildings in the working-class neighbourhood of Noailles, as a precaution.
There were concerns on Monday afternoon when part of an adjoining building collapsed.
Housing Minister Julien Denormandie said it was a "race against the clock" to find survivors and some 100 rescue workers with sniffer dogs are combing the rubble while a drone scanned the wreckage from above.
Google Maps images taken in recent months showed the two buildings had large visible cracks in their facades before they collapsed.
One of them had been condemned and, with its windows boarded up, was well-secured.
In theory it was unoccupied, officials said.
But neighbours feared there were people inside the other.
The incident has already sparked a political row over the quality of housing available to Marseille's poorest residents.
The neighbourhood is home to many buildings in a similarly poor condition, some of them run by slum landlords.
A 2015 government report said some 100,000 Marseille residents were living in housing that was dangerous for their health or security.