US media report that Tori Castillo, 39, is facing child abuse charges and the children are now with their father.
Onlookers in the car park instructed the five-year-old on how to open the boot from the inside, reports say.
Passersby had noticed the car shaking and noise coming from inside where it was parked outside a Walmart.
The incident happened on Thursday in Riverdale, Utah. It is not clear how long the children were in the boot.
Local police officer Casey Warren told KTVX: "It's never right to lock a child inside of a vehicle, let alone a trunk of a vehicle.
"Obviously there's a lot of things that could go wrong."
He praised the "good Samaritans" who helped the children get out.
Under Utah state law, leaving a child under the age of nine unattended in a vehicle is punishable by a fine or jail time. The law was enacted in 2011 after repeated cases of children dying unattended in hot cars.
A woman has been arrested in the US after allegedly locking her children, aged two and five, in the boot of her car while she went shopping.