Interior Minister Reverol said six "terrorists and hired killers" had been arrested, several vehicles seized and hotels raided. Neither the state leader nor the top government officials were injured in the explosion, he said.
One of the suspects had an outstanding arrest warrant for involvement in a 2017 attack on a military base that killed two people, Reverol said, an incident that followed four months of anti-government protests. "We have identified the people who made the explosives and prepared the weapons and their global links", Saab said.
"There will be no forgiveness", Maduro warned, for what a military statement said was an act of "barbarism in a desperate attempt to destabilize" the government.
Colombia's President Juan Manuel Santos has scoffed at the accusations, saying he was fully focused on his granddaughter's baptism on Saturday, while US national security adviser John Bolton said Washington was not involved in the blast. Security guards quickly moved in with ballistic blankets to protect Maduro.
On Sunday, White House national security adviser John Bolton said that the US had nothing to do with the incident and suggested the whole thing may have been "a pretext set up by the regime itself".
He called on Mr Trump to arrest the terrorists. Under Maduro - who has been in power since the 2013 death of his predecessor, Hugo Chavez - Venezuela has been in a near constant state of crisis.
The accusation was rejected by the Colombian Foreign Ministry, which called it "absurd". One of the drones was to explode above the president while the other was to detonate directly in front of him, he added.
But Nicmer Evans, a former government loyalist and now leader of the opposition Frente Amplio party, said he feared the government's measures "open the door to persecution and a wave of repression". The minister explained Sunday that they're also seeking to question at least one more person about the explosions that interrupted Maduro's televised speech to national guard troops a day earlier.
US President Donald Trump has been harshly critical of Maduro's leftist regime, saying it has "destroyed a prosperous nation by imposing a failed ideology".
But three local authorities said a gas tank exploded in a nearby flat, where smoke was seen streaming out of a window.
Maduro is deeply unpopular because of Venezuela's collapsed economy, hyperinflation that could reach 1 million percent this year and his autocratic style of governing.
The attack came as Venezuela is reeling from an economic and humanitarian crisis and Maduro has grown increasingly isolated.
"Venezuela will continue on the democratic, independent and socialist path", Maduro said. Hundreds of thousands of Venezuelans have left the country over this time, and past year, 125 people were killed across four months of clashes between Venezuelan authorities and anti-regime protesters.
Maduro this year brought forward to May presidential elections that - after they were boycotted by the opposition and key opposition figures were declared ineligible - handed him a new six-year term.