Regional police said officers shot Abouyaaqoub in Subirats, a small town 28 miles west of Barcelona, while investigating a "suspicious person" there. A bomb disposal robot was dispatched to approach the suspect, Catalan police said.
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Abouyaaqoub, 22, has been the target of an international manhunt since Thursday's van attack in Barcelona.
Authorities said Monday they have evidence that Abouyaaqoub drove the van that plowed down the city's famed Las Ramblas promenade, killing 13 pedestrians and injuring more than 120 others.
They said Abouyaaqoub, who was born in Morocco and has Spanish residency, also was suspected of carjacking a man and stabbing him to death as he made his getaway, raising the death toll between the Barcelona attack and a related attack hours later to 15.
Another vehicle attack early Friday by other members of what Catalonia regional police have described as a 12-member extremist cell killed one person and wounded several others in the coastal town of Cambrils. That ended in a shootout with police, who killed five attackers.
The Islamic State group has claimed responsibility for both attacks.
La Vanguardia newspaper earlier reported Abouyaaqoub was captured. Catalan police tweeted that there was an ongoing police operation in Subirats, but did not confirm if it involved the fugitive suspect.
Roser Ventura, whose father owns a vineyard between the towns of Sadurni d'Anoia and Subirats, said he alerted the regional Catalan police when they spotted a car crossing their property at high speed.
"The police told us to leave the premises and go home. We heard a helicopter flying around and many police cars coming toward the gas station that is some 600 meters from the property," Ventura said.
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Earlier Monday, regional police chief Josep Lluis Trapero said investigators have "scientific evidence" showing Abouyaaqoub drove the speeding van in Las Ramblas and killed the owner of a hijacked sedan on Thursday night.
He said the suspect walked through Barcelona for about 90 minutes after the van attack - through the famed La Boqueria market and nearly to Barcelona University - before hijacking the car. Abouyaaqoub is believed to have made his getaway in the stolen car with Perez's body inside.
Perez was parking his car, a Ford Focus, in a lot between 6:10 p.m. and 6:20 p.m. Abouyaaqoub stabbed him before 6:32 p.m., put him in the car's rear seats and drove away, Trapero said.
Trapero said Perez was already dead when Abouyaaqoub then rammed the car through a police checkpoint minutes later and police opened fire on his car.
The suspect ran over a police officer as the car evaded the checkpoint. About 7 p.m., police found the car and Perez's body 3 kilometers (nearly 2 miles) away from the checkpoint, near Sant Just Desvern, a town west of Barcelona, but Abouyaaqoub was nowhere to be found.
The Spanish newspaper El Pais published images Monday of what it said was Abouyaaqoub leaving the van attack site on foot. The three images show a slim man wearing sunglasses walking through the La Boqueria market.
Abouyaaqoub escaped and has not returned to his home in Ripoll, said Trapero. The manhunt for him reaches well beyond Spain's borders. Four other suspects have been arrested.
Regional authorities said Monday that 50 people were still hospitalized from both attacks, nine of them in critical condition.
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Abouyaaqoub was believed to be the lone attacker on the run by Sunday, but authorities hadn't confirmed his identity because they were having difficulty identifying the remains of at least two extremists who died Wednesday in an explosion at a house in Alcanar where explosives were being prepared.
The explosion destroyed the house, but police found remnants of over 100 butane gas tanks and materials needed for the TATP explosive, which has been used previously by Islamic State militants.
Those discoveries, and reports that Abouyaaqoub had rented three vans, suggested the militant cell was making plans for an even more massive attack on the city.
Catalonia's regional president, meanwhile, said regional and local authorities rejected the Spanish government's suggestion to place traffic barriers to protect the Las Ramblas promenade because they deemed them "inefficient."
Carles Puigdemont told La Sexta television the barriers wouldn't have prevented vehicles from entering the promenade at other points - and he said closing off Las Ramblas was impractical because emergency vehicles still needed access.
On Monday, mourners were still weeping and hugging each other as they visited the main memorial site of the Barcelona attack. Crowds of people continued to lay flowers, candles and heart-shaped balloons at the top of Las Ramblas and at other smaller tributes where the van created such carnage.
Las Ramblas regained some normality Monday, with throngs of people walking up and down, tourists arriving and residents going about their daily business.
"We have to stand strong in front of these betrayers, assassins, terrorists," said resident Monserrat Mora. "Because Barcelona is strong and they will not be able to prevail with us."
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