Because the partially dangling train was "very weak", rescue efforts were briefly paused at midnight and a crane had to be brought in.
"There were many people standing and sitting in the carriage", she said, adding that she hit the carriage's roof. The overpass was about five meters above the road in southern Mexico City.
Several train carriages plunged to the ground, crushing at least one vehicle, which was on a busy road underneath. She told reporters at the scene an additional two people had died, according to Reforma and Milenio newspapers.
There were still people trapped inside the train, though "we don't know if they are alive", said Sheinbaum.
Oscar López, 26, was searching for his friend, Adriana Salas, 26.More news: North Korea defectors defy South to launch anti-Kim leaflets
The injured are carried by stretcher after a raised subway track collapsed in Mexico City.
The accident unfolded at about 10.30pm Monday on the metro's Line 12 on the southeast side of the city.
Like numerous city's dozen subway lines, it runs underground through more central areas of the city.
Mexico's current Foreign Minister Marcelo Ebrard was mayor of the capital when Line 12 was constructed.
The accident occurred on line 12 of the metro railway in Mexico. The line had to be partly closed in 2013 so tracks could be repaired.More news: Women Make History As Nancy Pelosi, Kamala Harris Flank Biden For Speech
"What has happened on the metro today is a bad tragedy", tweeted Mexican foreign minister Marcelo Ebrard.
'Of course, the causes must be investigated and responsibilities defined.
It was not clear whether a 7.1-magnitude natural disaster in 2017 could have affected the subway line.
The Mexico City metro, one of the largest and busiest in the world, has had at least two serious accidents since it was built half a century ago.
In one of the worst accidents on the network, two metro trains rammed into each other leaving 23 dead and 55 injured in October 1975.More news: Arlene Foster to quit as Northern Irish first minister and DUP leader