A 10-meter (33-foot) tall pyramid was found within another 20-meter structure, which itself is enveloped by the 30-meter pyramid visible at the Mayan archeological complex known as Chichen Itza in Yucatan state.
The smallest pyramid was built between the years 550 and 800, engineers and anthropologists said.
The middle structure had already been discovered in the 1930s and dates back to the years 800-1,000, while the largest one was finished between 1050-1300.
The discovery suggests that the pyramid, known as "El Castillo" (The Castle), was built in three phases.
"It's like a Russian nesting doll. Under the large one we get another and another," Rene Chavez Seguro, the project's chief and a geophysics researcher at the National Autonomous University of Mexico, told a news conference.
Structures were built on top of each other for various reasons, including deterioration or the arrival of new leadership, said Denisse Argote, expert at the National Anthropology and History Institute.
The smallest pyramid was spotted using a non-invasive technique that consists in lighting the inside of the pyramid to see its interior without causing damage.The discovery could shed light on the original Mayan culture before it was influenced by populations from central Mexico, Argote said.
Last year, archeologists discovered that the Kukulkan pyramid was built atop a cenote, or underground river, which are common in the region and are sacred to the Maya.
The new evidence, in the journal Plos One, shows that humans living in South Africa more than 65,000 years ago sharpened rock into blades in the oldest known use of pyrotechnology to transform matter, researchers said.
"This marks a leap in knowledge and skill to use fire in the transformation of matter, which represents a considerable step in the technological evolution of man that is unique to this region," Anne Delagnes, a lead researcher of the study from the French National Center for Scientific Research (CNRS), told AFP.
Conducted at the Klipdrift Shelter -- a recently discovered Middle Stone Age site southeast of Cape Town -- the researchers analyzed heating techniques used to produce blades from silcrete rock.
The researchers found that 92 percent of the rock samples had traces of intentional heating -- a process that would harden and break open the rock, producing sharp pieces to make blades.
"The fire breaks the stone and removes internal impurities, minimizing the risk of fracture during the process -- a fairly sophisticated technique," said Delagnes.
Analysis suggested the stones were rapidly heated early in the process in open fireplaces at temperatures higher than 450 degrees Celsius (842 degrees Fahrenheit).
The humans were apparently making small stone tools with short blades on handles. Some even had multiple blades on one handle -- an ancient ancestor of the Swiss Army knife.
"It was an extremely innovative period in southern Africa," said Delagnes. Besides technological innovations including this form of pyrotechnology, she said there were already symbolic engravings of the first set of the elements on ostrich eggshells.
This most recent finding indicates that the use of intentional heat treatments was used in Africa between 50,000 and 65,000 years ago.
No traces of the technological innovation exist again until some 20,000 years ago when it was discovered in Siberia, and later on in Europe about 18,000 years ago, when heat was sometimes applied to finish tools.
Fire was applied to create blades more systematically in Western Europe just 11,000 years ago during the Neolithic period, which marked the beginning of human civilization with the appearance of agriculture and livestock.