The elections, clouded by North Korean nuclear threats and the multiple challenges facing Asia's fourth largest economy, came as President Park Geun-Hye enters the final stretch of her term in office.
With more than 90 percent of ballots counted, Park's Saenuri Party was predicted to win 124 seats in the 300-member National Assembly, Yonhap news agency said.
That leaves the party shy of the crucial 60 percent majority that would have allowed it to override opposition attempts to block legislation in the new assembly, making Park very much a lame duck.
"The people are deeply disappointed with us, but we've failed to read their mind," he added.
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The left-leaning main opposition Minjoo Party was projected to secure 121 seats and the splinter opposition People's Party was predicted to bag 39 spots.
It marked the first time in 16 years the conservative party has lost control of parliament, with the three opposition parties tipped to win a combined 165 seats, well over the majority.
Voter turnout was 58 per cent, up 3.8 percentage points from the 2012 election, and final official results were expected tomorrow morning.
Park has also fallen short on most of her key economic promises, a failure she puts down to legislative inaction.
But critics accuse her of skewed priorities, poor decision-making and a dogmatic style of leadership.
Political power in South Korea is firmly concentrated in the presidency, with incumbents limited to a single five-year term.
Dissatisfaction is especially high among young people, with the jobless rate among those aged 15-29 at record levels.