The explosion, which came nine months after ETA declared a permanent ceasefire, injured 19 people, with two others reported missing.
"I have ordered the suspension of all initiatives linked to developing" talks with ETA, Zapatero said after interrupting a family holiday to return to the capital.
The prime minister did not say he was closing the door on a negotiated settlement but he stipulated that ETA must "show an unequivocable desire to renounce violence."
The interior ministry meanwhile said two people, both from Ecuador, were missing after the blast, which ETA claimed in one of an early morning series of anonymous telephone calls.
If either missing person were to be found dead then Spain would mourn its first ETA-related fatality since May 2003, when two policemen were killed in a car bomb attack in the Navarra region adjoining the northern Basque region.
ETA called its ceasefire on March 22, since when the Socialist government has attempted to broker a dialogue with the group.
But continuing low-level violence and the October theft of a stash of handguns in southern France blamed on ETA has hampered attempts to foster peace.
Interior Minister Alfredo Perez Rubalcaba gave a blunt assessment in the government's first reaction.
The attack "breaks the ceasefire," Rubalcaba told reporters.
"I roundly condemn this blast which interrupts, which breaks nine months since ETA committed an act of violence.
Arnaldo Otegi, spokesman of ETA's banned political mouthpiece Batasuna, insisted the peace process was still alive.
"From our point of view, the peace process is not broken," Otegi told a news conference in the Basque city of San Sebastian.
But he did not condemn the attack and blamed the government for "not making a single gesture" to hardline nationalists during the ceasefire.
The bomb, in a Renault van, exploded at about 9:00am (0800 GMT) in a car park at Barajas airport's terminal four, inaugurated earlier this year, as passengers streamed in to take New Year holiday flights.
"I heard a big boom," Jaime, a groundstaff employee with national airline Iberia, told AFP.
He described the day's events ads "nervewracking."
Emergency services said four people, including two police, were treated in hospital for what police described as "slight injuries".
Fifteen others received treatment for very minor cuts and hearing problems after the explosion showered glass shards over a wide area.
Dozens of flights were cancelled and many at other terminals were delayed as relatives of passengers worried amid the growing chaos.
"My cousin, Anna, was supposed to be getting a flight to Quito. She phoned us from inside the terminal. She's frightened as she is travelling alone," one Ecuadorean woman, who gave her name only as Rocio, told AFP, as a huge pall of thick, black smoke billowed from the terminal building.
Police sealed off the area after an anonymous caller warned Basque road safety authorities about the bomb, a Basque official said, before a second warning given to the Madrid fire brigade and then a third call confirming the imminent blast in ETA's name.
ETA has been fighting for almost four decades for a Basque state and is blamed for some 850 deaths over that period.
Zapatero had Friday forecast that "the situation will be better in a year," amid "discreet" negotiations.
But the conservative Popular Party (PP) opposition party saw his optimism as misplaced after Saturday's blast.
"ETA is a criminal organisation which does not want any peace," said PP leader Mariano Rajoy, who has slammed Zapatero's policy of dialogue.