Spokesman Bahram Qassemi on Saturday expressed regret over the attack, which killed at least 21 people and wounded more than 80 others on Thursday.
The Iranian official also expressed sympathy with the families of the victims of the attack, the worst in Bogota in 16 years.
The Colombian government declared three days of mourning on Thursday, Presstv reported.
Colombia’s Defense Ministry said the "terrorist act" was carried out using a vehicle packed with 80 kilograms of explosives.
President Ivan Duque described the attack as a "crazy terrorist act" and ordered reinforcements to Colombia's borders and routes in and out of cities "to identify the masterminds of this terrorist attack and their accomplices."
On Friday, the government blamed the National Liberation Army (ELN) Marxist guerrilla group for the bombing.
Colombia’s Defense Minister Guillermo Botero called the car bombing as a long-planned "terrorist attack committed by the ELN."
The attack is a major setback to two years of peace talks with ELN. The first round of negotiations was hosted by Ecuador and Cuba is the current host.
Following the bombing, President Duque said he was reinstating arrest warrants for 10 ELN members who are part of the group's delegation to the Cuba talks. He said he was revoking "the resolution creating the conditions that allow their stay in that country."
"The national government knows and understands that the ELN has no will for peace," Colombia's peace commissioner Miguel Ceballos told reporters earlier.
Botero said he had "full evidence" that the attacker, earlier identified as Jose Aldemar Rojas Rodriguez, 56, has been a member of the ELN for more than 25 years.
According to Botero, Rojas was known by his nickname "One-hand Kiko" for losing his left hand in an explosion and was an intelligence chief in an ELN unit operating in the department of Arauca, on the border with Venezuela.
"This was an operation that has been planned for the past 10 months," Botero said, calling the guerrilla group the "intellectual authors" of the attack.
The ELN has not yet commented on the accusations.
Attorney General Nestor Humberto said another suspect also linked to the ELN, named Ricardo Carvajal, was arrested overnight in Bogota.
During decades of bloody civil war between the government and various leftist rebel groups, car bomb attacks were frequent. Thousands were killed or wounded in the bombings.
The worst of such wars, however, ended when Bogota reached a peace deal with the Revolutionary Armed Forces of Colombia (FARC) in 2016.
Furthermore, the South American country has myriad crime gangs, some of which operate across large swaths of rural areas and others in major cities. Many of these gangs are involved in the production and trafficking of cocaine, largely to the United States and Europe, as well as extortion and other crimes.