The closure, due to last 36 hours, will affect five million people, or a quarter of the city's population.
Unusually low rainfall last year and major leakage are blamed for leaving reservoirs less than half full.
Hundreds of water trucks have been deployed in the areas worst affected by the cuts.
The local government says it will carry out emergency repairs to the water supply network.
More than 50% of the water carried by the pipeline leaks out before it reaches its destination.
This is the third time the capital has faced such a drastic form of water rationing this year, the BBC's Stephen Gibbs in Mexico City reports.
FLORIDA's worsening drought sparks water fights - A worsening drought is sparking battles over dwindling water supplies, with Florida's southwest coast demanding relief for rivers and estuaries. Everglades marshes and Big Cypress swamps are drying up. Estuaries at the mouths of the St. Lucie and Caloosahatchee rivers are turning too salty. Lake Okeechobee, brimming from Tropical Storm Fay less than a year ago, is slipping into the low zone again. Overall, the region has received less than 30 percent of its normal rainfall. ''If we don't get an inch of rain in the next three weeks, this will be the driest dry season on record." Water managers say the region lucked out last year when Tropical Storm Fay dumped 20 inches north of Lake Okeechobee, erasing the last long and damaging drought in a few days. ''That's all we have between us and disaster.''