Chung had apologised for his actions and his lawyers had argued he be given a suspended sentence - meaning he would not actually serve prison time unless involved in other crimes.
Last year he admitted to having a role in setting up slush funds through affiliates of Hyundai.
Passing sentence judge Kim Dong-oh said Chung's actions were "clearly criminal acts" that required a firm punishment.
"The court decided a strict execution of law is necessary to eradicate illegal and anti-market practices in the past and help South Korea build a more advanced economy," he said.
Hyundai shares down by more than 3 per cent.
Analysts expect South Korean economy to be strongly affected.
Combined exports by Hyundai and affiliate Kia account for nearly 7 per cent of South Korea's total exports.
Possible management vacuum.
Analysts had expected court to hand down suspended jail term to leave Chung at Hyundai's helm.
Management shortcomings at South Korea's powerful "chaebol" or family-run conglomerates highlighted.
Chaebol helped rebuild the economy after the 1950-53 Korean war but were partly blamed for 1997-98 Asian financial crisis.
Three other Hyundai officials facing similar charges were also convicted but all given suspended sentences.
The ruling is being seen as another blow for a company contending with a rising won and continuing unrest from labour unions.
Analysts had expected the court to hand down a suspended jail term to leave Chung at the helm of Hyundai, given the group's importance to the South Korean economy.
According to company data exports by Hyundai and its affiliate Kia Motors account for nearly 7 per cent of total exports from South Korea, Asia's third-largest economy.
Chung is the son of Hyundai group founder, whose post-World War II auto-repair shop burgeoned into a sprawling conglomerate.
He was arrested last April on allegations that Hyundai and its affiliates set up slush funds to pay for political favours.
Chung will remain free on bail for the time being and does not face immediate arrest.
He was absent from work for more than two months after being jailed following his April arrest and entering a hospital for a health exam. He was granted bail in June and returned to work in July.