Amanda Hawkins, 19, left the girls, aged one and two, in the car at 21:00 on Tuesday (03:00 GMT Wednesday) to visit friends nearby, police said.
Her daughters cried during the night but she ignored them, a sheriff said, and returned only at noon the next day.
Ms Hawkins has been charged with two counts of child endangerment.
Kerr County Sheriff Rusty Hierholzer said it was the worst such case he had seen in 37 years on the force.
Hot car deaths: The children left behind
Ms Hawkins left one-year-old Brynn Hawkins and two-year-old Addyson Overgard-Eddy in the car to visit a 16-year-old male friend and others at a house in the town of Kerrville, 65 miles (105 km) north-west of San Antonio.
The sheriff said the male friend had at some point slept in the car alongside the children but they were not let out.
Ms Hawkins finally took the children out at noon the next day and found them unconscious.
She tried to bathe them, the sheriff said, but fearing she would get into trouble, did not seek medical help immediately.
Only after a friend suggested it did she take them to the nearby Peterson Regional Medical Center.
She reportedly told staff that she, the teenage male and the children had been at a nearby lake and the girls had "collapsed after smelling flowers".
"They thought maybe they'd gotten into something poisonous - that's what the story was," Sheriff Hierholzer told the CNN affiliate station KABB.
"She left them in the car - intentionally in the car - while her and the 16-year-old male friend were in the house," he said.
The girls were quickly taken to the University Hospital in San Antonio but died at about 17:00 on Thursday.
Police say the charges may now be upgraded.
Ms Hawkins' husband was reportedly not present during the incident.
Two young sisters have died in Texas after their mother allegedly left them in a car for 15 hours in temperatures of up to 32C (90F).