Five-year-old Pascual Saraos Jimenez and 6-year-old Miguel Saraos Jimenez disappeared Sunday night in the Indian village of Jochich, about 100 kilometers (60 miles) northeast of the state capital, Tuxtla Gutierrez.
Emergency crews have been trying to reach them for days, using heavy machinery from Mexico's state-run oil company, Pemex, to widen the mouth of the narrow cavern, estimated at 25 to 40 meters (27 to 43 yards) deep.
Rescue authorities had earlier heard the two boys talking, but eventually their voices disappeared. Heavy rains also hampered the search, and officials said an underground river filled the cave with water.
Authorities planned to drain the cave once it stopped raining, and begin searching for the boys' bodies.
The rescue operation had initially met with resistance from machete-wielding residents of Jochich who thought officials were digging for gold, not just removing earth.