Armed police, dog units and a helicopter were scrambled when the children's dad raised the alarm on Saturday afternoon.
The car was stolen from the man's driveway in Birmingham at around 5pm with his two boys, aged two and four, inside.
The stolen Seat Leon was then seen driving the wrong way down a dual carriageway before armed officers brought it to a halt on the A38 Bristol Road near Belgrave Interchange.
Paramedics from West Midlands Ambulance were sent to the scene and checked over the children, who were unharmed and reunited with their parents at the roadside.
Meanwhile the two suspects ran from the Seat but were soon detained and arrested by officers, West Midlands Police said.
Two boys, both aged 15 and from Birmingham, have been remanded in custody to appear before Birmingham Magistrates court tomorrow morning .
The pair, who cannot be named for legal reasons, will both stand accused of two counts of kidnap and aggravated theft of a motor vehicle.
One of the teens has also been charged with dangerous driving, driving without a licence and driving without insurance.
Chief Inspector Lee Wiggan, the force incident manager, said: “This type of incident is every parent’s worst nightmare, but thankfully we were able to stop the car and reunite the family less than 15 minutes after it was stolen.
“It’s a fantastic outcome to what was a very serious, urgent incident and my thanks go to the officers involved as well as West Midlands Ambulance Service for their support."
David Jamieson, the West Midlands Police and Crime Commissioner, praised the quick response of the officers involved.
He said: “To be able to find and stop this stolen vehicle, which still had the owner’s two young children inside, in under 15 minutes is testament to the speed and professionalism of West Midlands Police.
“With the lives of a four and a two-year-old in danger the force wasted no time in scrambling a range of highly skilled officers, including armed police and the helicopter team.
“It was this speed and determination which potentially saved the lives of the two children in the back of that vehicle and led to the arrest of the two 15-year-olds.
“I’d like to congratulate and thank our hard working officers for their heroic efforts. They work 24/7 to keep us all safe and thankfully this story has a happy ending.
“I wish the family well.”