The reptile, thought to have been brought in illegally as a pet and later released in a river in the region's rural New Territories area, swam into a trap on Thursday.
"Yes, we've got it," a spokesman for the Agriculture and Fisheries Department confirmed.
The 1.5m animal, named Croc Croc Chan after the family that first spotted it in October, became a media star in a region better known for its gleaming skyscrapers than its wildlife.
Not long after the reptile was first sighted, radio callers elected it "Personality of the year."
Its fame soared after it managed to give hunters from Australia and mainland China the slip. It attracted hundreds of tourists a day after newspapers splashed its picture on their front pages.
Hong Kong has no native crocodile species and this rare visitor enchanted residents, who are more accustomed to seeing such creatures on television - or as material for designer handbags and shoes.
Experts said Croc Croc Chan, a salt-water crocodile, could grow to a length of eight metres. Its species has the worst record for attacks on people.
The reptile was taken to an animal centre to be examined by government veterinarians.
It was not immediately clear what the government planned to do with Croc Croc Chan. "We will have to decide later," said the spokesman.