The "highest temperature since records have been kept" was recorded Saturday afternoon at the Tacubaya observatory, the National Meteorological Service said.
The previous record of 34.4 degrees Celsius was observed the day before at the same station in the capital, the weather service added.
Mexico has recorded 48 deaths due to intense heatwaves hitting the country since March, the government said on Friday.
More than 950 people have suffered various health effects over the same period, as of May 21, according to the health ministry.
The eastern coastal state of Veracruz recorded the highest number of deaths, with 14, followed by Tabasco, San Luis Potosi and Tamaulipas with eight each.
Last year, Mexico reported a record 419 heat-related deaths in the hot season, which runs from March to October, in a country of 129 million people.
It is not just humans that are suffering -- in southern Mexico dozens of howler monkeys have dropped dead, apparently due to the heat.
- 'Warmest year in history' -
Scientists from the National Autonomous University of Mexico warned on Wednesday that in the next two weeks intensifying heat could bring new record temperatures to the capital.
This year is on course to be "the warmest year in history," Francisco Estrada, coordinator of the university's Climate Change Research Program, said at a press conference.
Mexico City, which sits at 2,240 meters (7,350 feet) above sea level, has traditionally enjoyed a temperate climate and few homes have air conditioning.
But the capital has repeatedly seen fresh high-temperature records this hot season, with the mercury reaching then-records of 34.3 C on May 9 and 34.2 C on April 15.
The intense heat -- which has emptied stores of bottled water and ice packs in the capital and its metropolitan area, where about 22 million people live -- combined with the scarce wind, has triggered pollution in the megacity where around 6.5 million vehicles circulate.
President Andres Manuel Lopez Obrador has described this year's heat as "exceptional."
"It's a very regrettable natural phenomenon related to climate change," he said.
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