The victims -- two Colombians and a Frenchwoman -- perished when a device exploded in a ladies' toilet in the crowded Andino shopping center in Bogota on Saturday. At least nine people were also wounded, officials said.
President Juan Manuel Santos called the incident a terrorist attack.
Rebel groups condemned the blast and said it was an attempt to undermine their steps along with the government to end Colombia's half-century civil conflict.
"There was a strong boom and the floor shook," said shop worker Milena Carcenas.
"There was smoke coming out of the bathroom. People were coming out of there covered in ash."
National police chief General Jorge Nieto told reporters "a device" was placed "behind one of the toilets in the women's bathroom."
Witness Andres Bermudez, his hands still trembling after the attack, said people were crying at the scene.
"It's a miracle I'm alive," he told AFP outside the mall, which he was visiting to pay some bills.
The last active rebel force, the National Liberation Army (ELN), meanwhile, has started talks with the government, though confrontations with state forces have been continuing.
"Those who want to rain on the peace parade will not succeed," said Santos, who won a Nobel Peace Prize last year for sealing an accord with FARC leaders.
"If this (bombing) is that kind of gesture, then rest assured that we will pursue those enemies of peace without rest and without quarter," he said, speaking at the site of the blast.
A redrafted agreement from Santos and the FARC has since been pushed through congress.
"Terrorists are not going to change our ways," Santos said, urging Colombians to continue their normal lives and enjoy the Father's Day holiday, though he did not identify who could be behind Saturday's attack.
A security council meeting will take place Sunday "to discuss further steps to ensure calm in Bogota," he added.
Bogota Mayor Enrique Penalosa called Saturday's incident "a cowardly terrorist attack."
The leftist ELN said on Twitter it "condemns this deplorable incident," noting that the attack was "against civilians."
"We share the pain and stand in solidarity with the victims," the group wrote. "The state should investigate thoroughly to identify those responsible."
The leader of the communist-inspired FARC, Rodrigo Londono -- known as Timochenko -- also denounced the explosion.
"This act can only come from those who want to close the roads of peace and reconciliation," he wrote on Twitter.
The blast was the second major attack this year in the Colombian capital.
Colombia's civil conflict erupted in 1964 over land rights. It has drawn in leftist guerrillas, right-wing paramilitary groups and state forces.
Analyst Victor Currea-Logo of Colombia's National University said it was unlikely either of the leftist groups involved in the peace drive would have carried out the attack.
But he told AFP: "There are some far-right paramilitary- style groups who have been responsible for killing civil leaders and for actions against the peace effort."
Efforts to disrupt the process, however, is unlikely he said, citing public support for peace.
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