Two men, aged 25 and 33, were shot dead in the attack at 5 a.m. (0300 GMT) in the sprawling neighborhood of Hanover Park.
Earlier, at about 2:45 p.m., a 27-year-old man was wounded in a separate shooting in Mitchells Plain.
“I am afraid for my children,” said a 65-year-old grandmother, speaking on condition of anonymity, adding that she suspects her backyard is being used for surveillance at night.
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“I can't sleep the whole night,” he said, adding that his daughter leaving at 4 a.m. makes him “very anxious.”
Retiree Malvin Gordon, 69, said shootings happen all the time, involving children going to and from school.
The deployment was a welcome relief, he said, adding that the army's “lone presence” had forced gang members to stand back.
The Cape Flats saw one of its deadliest weeks ever last August when police recorded 59 murders in seven days.
Violence elsewhere In February President Cyril Ramaphosa announced the deployment to boost the country's struggling police force, saying crime was one of South Africa's biggest threats.
Excluding war-torn countries, South Africa has the world's highest murder rate, with an average of 60 murders recorded every day.
According to the plan tabled in Parliament, the deployment, codenamed “Operation Prosper”, would last a year and cover five of the nine provinces, including Gauteng, home of the financial capital Johannesburg.
It mobilizes more than 2,200 troops to support the police in tackling the increase in crime and illegal mining.
From imposing strict COVID-19 lockdowns in 2020 to deploying troops during deadly riots sparked by the jailing of former President Jacob Zuma in 2021, South Africa has repeatedly turned to the military in times of crisis.