The 38-year-old woman survived the crash but was seriously injured. Rescuers and police found the bodies of her four-month-old twins and six-year-old daughter in the wreckage of the car.
Officers had on Tuesday followed her from her house in the rural area of Freising near Munich after her partner called them and said he was worried she might do something to the children.
He said she had sent him a message saying she was going to kill their baby boy and girl, and the daughter who was from her previous marriage.
The police found her but she drove off and fled to the A92 motorway where the officers said they followed at a distance - and saw as she seemed to deliberately cause a crash, flipping the car over several times.
An autopsy seemed to confirm the father's fears - the children had been suffocated before the crash and were already dead when the woman put them in car.
She was flown to a nearby hospital with serious injuries and later arrested and questioned on suspicion of three counts of murder. She confessed to wanting to kill herself, but did not say why.
The woman has another child who lives with her former husband - the father of the girl found in the car.