The explosion occurred in an area of northern Bogota where restaurants and retail stores are plentiful.
City police chief Rodolfo Palomino says the bomb appeared to be about 11 pounds (five kilograms) of explosives and was placed in an automatic teller booth adjacent to the store.
The victims' identities were not immediately known.
The government is offering a $45,000 reward for information leading to those responsible for Tuesday's blast.
Defense Minister Juan Manuel Santos says there's no evidence it was leftist rebels.
Some officials say the store had been the object of extortion.