The unnamed pyramid has the same sized base as the giant Pyramid of the Moon at the famous archaeological site of Teotihuacan, an hour's drive northeast of the capital, which is known as the City of the Gods and is Mexico's biggest, ancient city.
Archaeologist Jesus Sanchez said the latest find was built by the same people who constructed Teotihuacan between 400 and 500 AD, and has evidence that it was used for ceremonial purposes.
"The structure is protected because it is beneath two feet (60cm) of earth," Mr Sanchez told a radio station.
But half the pyramid has been destroyed as the hill has been used for decades every Easter for a gory re-enactment of the crucifixion of Christ. The religious celebration is attended by hundreds of thousands of believers.
Houses built illegally on one side of the hill have also damaged the pyramid, which is about 18 metres tall, half the height of the Pyramid of the Moon, said Mr Sanchez, archaeologist with the National Institute of Anthropology and History.
The site will not be fully explored because it is now considered a religious centre in its own right, he said.
The north side of the pyramid opens out into a large square, whose limits are defined by a low stone wall. On the south side there is another small temple, with evidence of holes in the walls for offerings to be placed.
The site overlooks a vast suburban neighbourhood, considered one of Mexico City's poorest and most dangerous. A periphery fence is to be built around it to stop vehicles from entering and damaging it more.
The find is one of many examples in Mexico of important pre-Hispanic sites that have become Catholic places of worship.
After the Spanish conquest, conquistadors and envoys of the church superimposed their beliefs on indigenous life.
Churches were built atop ancient shrines and pyramids in sites around Mexico, including Chalma and Cholula near Mexico City.
The Mexican capital's massive cathedral was built from stone from pyramids flattened by the Spaniards.