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.