The girl disappeared from Primark in Northumberland St on Wednesday at around 5pm.
Northumbria Police said the teenagers and the girl were “complete strangers”.
The girl’s disappearance sparked a city-wide search after officers found she had left the store with the two older girls, leaving her mother “incredibly” distressed.
Police trawled through CCTV from Newcastle City Council, shops, Newcastle University, bus companies, the Metro and their own cameras in search of the child.
She was eventually found nearly three miles (4.8km) away and over an hour later in Gosforth, north Newcastle, by a police officer.
The alleged kidnappers, aged 13 and 14, were arrested on suspicion of child abduction and taken in for questioning.
A force spokesman said yesterday they were still in custody. He would not comment on any apparent motive.
Chief Inspector Dave Gould said: “Thankfully the child was quickly located by officers and then reunited with her mother. This has been an incredibly distressing time for the girl’s family and specialist officers are working with and supporting the family.
“We mobilised all available local police resources to make sure the girl was found as quickly as possible and also included assistance from the public, and many of our partner agencies including Newcastle local authority and university as well as staff from retail premises, bus companies, train station, and Metro system.
“I would like to thank all of those involved for their help in finding this little girl and helping reunite her with her mother. Our inquiries will now continue to establish the circumstances of what happened and speaking to the two teenage girls in custody regarding the incident.”
A spokeswoman for Primark said they are “co-operating with the police on the investigation”.