It happened around 8 p.m. Thursday outside the PetSmart on Washington Avenue.
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The boy's mother went into the store and left the engine running, according to police.
She returned approximately a minute later to find the car was stolen.
Police responded to the scene. The mother told officers that her son was sleeping in the back seat.
"It was a crime of opportunity. Someone saw this vehicle, engine running, they stole the car, more than likely didn't realize there was child asleep in the back seat," Philadelphia Police Chief Inspector Scott Small said.
Authorities put out a call over police radio for the stolen vehicle, a 2012 gray Toyota RAV 4 with New Jersey tags.
They were soon notified that a 5-year-old boy had been dropped off at Broad and Wharton streets.
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Officers found the child and reunited him with his mother.
He was not injured.
"We're very fortunate the child is OK," Small said.
Police say witnesses described the suspects as three juvenile males.
Police say there were commercial surveillance cameras at both scenes, where the SUV was stolen and where the child was dropped off. They are hoping video will help lead them to the suspects.
Small says police see this type of incident occurs several times a year, where a car is left running with a child inside and then is stolen. Usually, he says, they find the child and vehicle a short time later. This time, however, they have yet to locate the SUV.