"When we did the excavations [in the Temple of Tlaloc], we saw that the stones were loose, the core was not stable", archaeologist Barbara Konieczna from the centre of INAH-Morelos, said.
Experts say it would have been around six meters long and four meters wide.
The upper part of the pyramid was heavily damaged during the 2017 quake, so researchers from Mexico's National Institute of Anthropology and History (INAH) wanted to give the ancient construction a quick check-up, using radar to identify whether its internal structure had been disturbed by the rumbles.
A devastating natural disaster that rocked central Mexico in September a year ago has revealed the remnants of a temple inside an Aztec pyramid.
The discovery could shed new light on the Tlahuica civilisation, according to experts.
Archeologists believe the temple was built between 1150 and 1200 and was dedicated to the Aztec rain god Tlaloc.
'This finding changes the chronology of Teopanzolco, since the basement was first discovered and then, in the image of that type of construction, the Templo Mayor was built in Tenochtitlan.
"There was no news, until now, of the existence of a substructure within the pyramidal structure", said INAH Director Isabel Campos Goenaga at a press conference.
She added: "The floor of both shrines sank and bent, which also put their stability in danger".
When the institute carried out studies with radar to examine the pyramid's structure, they found traces of the newly discovered Tlaloc temple. Huitzilopochtli was the Aztec god of the sun and war.
The magnitude 7.1 quake on September 19 caused parts of the pyramid to sink or lean.
View of the substructure inside the Teopanzolco pyramid in Cuernavaca, Morelos State, Mexico on July 11. The majority of those killed by the quake were in the capital, but others were killed in the states of Puebla and Morelos.
More than 200 people were killed in Mexico City and many people were trapped under rubble when buildings were toppled.