His right-wing political party, the Democratic Center, won the most seats of any political party.
The peace agreement has polarised the country because Farc rebels fought the government for more than 50 years and more than 260,000 people were killed in the conflict.
Sunday's vote was seen as a barometer for a fiercely contested presidential election in May. "A long war has generated lots of fear and rancour towards them".
Duque, a protégé of former president Alvaro Uribe, backs foreign investment and an aggressive security strategy meant to combat the country's remaining rebel group, which regularly bombs oil pipelines.
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For first time in more than half a century, South American country has been able to go to vote without existence of a cruel armed conflict in its territory.
The FARC, which signed a peace pact with the government 15 months ago, is assured 10 congressional seats, five in the Senate and five in the Chamber of Representatives, as part of its peace agreement with the government, but could garner more depending on the number of votes the party gets.
The National Liberation Army, or ELN, said Monday that it was ready to resume peace talks with the Colombian government, which have been suspended since January 9, prompting Colombian President Juan Manuel Santos to confirm the news and officially announce restarting the negotiations with the leftist rebels. His Party of National Unity, which was the biggest political movement in the outgoing congress, finished fifth overall.
The results are likely to lead to a last-minute scramble among presidential candidates to form coalitions to better position themselves ahead of what is seen as a wide-open presidential race. Left-wing candidate Gustavo Petro, who has been riding high in the polls despite an intense campaign against him, easily won the primaries for his coalition while Uribe-backed Senator Ivan Duque topped his opponent from the Conservative party by over 40 points.
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Two candidates under pressure to join forces are Humberto de la Calle, who was the government's chief peace negotiator, and former Gov. Sergio Fajardo.
He staked his reputation on securing a peace deal with the Farc and launched peace talks with the group two years after taking office in 2010.
"Our results were very positive", Petro told his followers.
"There's now sure to be at the presidential level a shake out of candidates over the coming weeks as we approach the first round - Petro can't yet be completely discounted but he looks further from his goal today compared with Friday", said Rupert Stebbings, managing director of equities at Grupo Bancolombia. He has also called for tougher controls on the FARC's finances.
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Duque and Vargas Lleras, from the Radical Change party, have strong party machines behind them and can count on backing in Congress should either of them win the presidency. The pro peace deal vote is now split among Gustavo Petro, Sergio Fajardo and Humberto de la Calle.