The 20-minute drill, which began at 2:00 pm (0500 GMT), was aimed at "preparing for a quick evacuation in the event of an air raid attack such as North Korea's missile provocations", Seoul's interior ministry said.
As sirens went off across South Korea, pedestrians were instructed to move to nearby shelters or underground facilities. There are around 17,000 designated shelters across the country.
In regions closer to nuclear-armed North Korea, the government prepared a more intense drill, with chemical, biological and radiological training, including instructions for putting on a gas mask and using emergency food rations.
Participation in the drill was not mandatory, but those who took part said the training was important for raising awareness about the security situation on the Korean peninsula.
"If North Korean soldiers suddenly invade, confusion will lead to more casualties," said barista Ahn Tae-hong, adding: "That is why we must train well."
Choi In-ho, a 62-year-old travel agent, said the drill was "a bit inconvenient", but necessary.
"We are always in confrontation with North Korea, but we've become too complacent about it," he told AFP.
But for others, it was business as usual.
One user on the social media platform X wrote: "I heard the siren so I just cranked up my music louder."
The civil defence exercises were launched in 1969 following a raid by North Korean commandos into the presidential compound in Seoul, but they have been suspended since 2017 -- initially due to a thaw in relations with Pyongyang, and then because of the Covid-19 pandemic.
South Korea's widely read Chosun Ilbo newspaper said the resumption of the civil drills was "urgent" in the wake of various natural disasters and the growing nuclear threats from the North.
"It is no exaggeration to say that the Korean people's ability to prepare for disasters is close to '0'," the paper said in an editorial.
"How many people are aware of what to do in the event of a North Korean missile attack, earthquake or fire?"
The civil defence drills come just months after the government mistakenly sent an emergency evacuation alert across Seoul over a North Korean rocket launch, triggering widespread panic.