The Japanese manufacturer insists it has complied with regulations.
“We are disappointed with the court’s decision," a statement from Nissan said.
"Nissan Korea maintains that it has complied with all existing regulations and did not use an ‘unjustified arbitrary set-up’ or an illegal defeat device in the Euro 6 Qashqai.”
The South Korean government however ruled that the so-called device lowered nitrogen oxide (NOx) emissions under testing, leading to excess NOx emissions when the system deactivated under normal driving conditions.
Qashqai sales in South Korea have been halted and 814 models have been recalled.
Nissan was fined around £300,000 last year after being accused of cheating on its emissions tests, but refuted the claims and later sued the government's environment ministry.
When it was originally accused, the manufacturer strenuously denied accusations by the government that it had used an emissions defeat device.
The South Korean government independently tested real-world emissions of 20 diesel cars in the wake of the Volkswagen dieselgate scandal, and it was believed the cheat device discovered was linked to Nissan's emissions-reducing Exhaust Gas Recirculation (EGR) system, which stopped operating when the engine's temperature reached 35deg Celsius.
"Usually, some cars turn off the emissions reduction device when the temperature reaches 50deg Celsius, to prevent the engine from overheating,'' a government spokesman said at the time. “The Qashqai was the only vehicle that turned it off at 35deg.”