In addition, Ruth Burger, 65, of London, Ont., is also charged with two counts of criminal negligence causing bodily harm in relation to injuries suffered by the girl's younger sister and their pregnant mother whose baby died after delivery by emergency C-section.
Police said there were no legal grounds for a charge in connection with the newborn's death.
"The definition of the Criminal Code has some stipulations that a person becomes a person, essentially, when it is born from its mother in a living state," said London police Sgt. Amanda Pfeffer.
The tragic incident occurred July 25 when a car going backwards smashed through the front doors of the Costco store, striking the trio.
Addison Hall, 6, was fatally hurt. Her three-year-old sister, Miah, and their mother, Danah McKinnon-Bozek, who was eight months pregnant, were injured.
McKinnon-Bozek's baby was delivered by C-section immediately after the crash but died in hospital on Aug. 1.
She has since been released from hospital while Miah remains hospitalized in good condition, police said.
Pfeffer would not say whether mechanical failure or a possible medical incident involving the driver factored in the crash, saying the matter is now before the courts.
Burger has been released from custody and is scheduled to appear in court on Sept. 16.
Police said their investigation was continuing and officers were looking to speak to witnesses who were in the store parking lot at the time of the crash.
"We are at a point where we have laid charges in this case but that does not mean that the investigation is over," Pfeffer said.
"We have surveillance video available to us and there are people that we are certain witnessed what transpired who haven't come forward yet to speak with the police."
Two other people suffered minor injuries in the crash as did the driver.