"The toddler's sister attempted to help him when the statue began to fall," said San Francisco police spokesman Officer Gordon Shyy.
The boy, Kayson Shelton, of Draper, Utah, was taken to the hospital with a bloody nose. He died hours later of internal injuries.
Authorities said the store, Majestic Collection, had been cited for placing merchandise beyond a blue line that marks the public sidewalk.
"This is an unfortunate and tragic incident. Majestic Collection is and has been co-operating with all investigative agencies. Our hearts and prayers are with the family," the store said in a statement.
They can't put merchandise outside a certain area of their storefront," Shyy said. "This is a very heavily travelled area so the Port Authority has created some guidelines where they can place their merchandise. That way it doesn't impede the traffic for a number of pedestrians maybe walking."