Ex Colombian President Alvaro Uribe's Democratic Center Party has won numerous seats in the Congressional Elections for the 106 members House of Representatives and 102 seat Senate, but not an overall majority.
Casting a shadow over the FARC's political ambitions is the recent decision to withdraw its candidate from the presidential race for health reasons.
Another candidate who has backed the peace deal is Gustavo Petro, a leftist former mayor of Bogota who has promised to raise taxes on the rich and unseat the country's political establishment.
Duque, 41, supported by former President Alvaro Uribe and his Democratic Center party, backs foreign investment and an aggressive security strategy meant to combat Colombia's remaining rebel group, which regularly kidnaps and bombs oil pipelines.
While Santos won the Nobel Peace Prize in 2016 for his peace brokering efforts, not all Colombians are convinced that negotiating with the rebels is the right strategy, with more hardline groups saying the rebels should be military defeated. He won 2.8 million votes in his primary on Sunday.
Both left and right-wing coalitions chose their candidates in primaries over the weekend.
"Our results were very positive" Petro told his followers after hearing of the first results.
Sunday's primaries - in which Duque won nearly 42 percent more votes than Petro did - were considered a better test of voter support than often inaccurate opinion polls, although some voters will have participated strategically and may not back either victor in the presidential vote.
The peace accord with the Revolutionary Armed Forces of Colombia (FARC) guarantees their new political party 10 of the 280 seats in the new Congress.
Candidates were mobbed by angry crowds at rallies and the party had to cancel its public meetings. The group is guaranteed 10 seats in the body through 2026 under the terms of the peace deal.
The Farc, who kept their acronym when they transformed from an insurgency into a political party, took a meagre 0.33% of the vote.
"Although no party won a majority outright, together the three right-wing parties have 50 seats in the senate, which will make passing a law very hard without at least some of their support", Steele said. Analysts believe that a conservative government could try to block part of its implementation, including agrarian reform and a truth and reconciliation deal.
In 1964, FARC rebels launched an insurgency against the Colombian state in response to the government's brutal suppression of a peasant uprising.
"As leader, but above all as a human being, I cannot give up doing everything I can, until I have exhausted every recourse, so that no more lives are lost, no more people are injured or mutilated, no more damage is inflicted on infrastructure or wildlife due to the conflict with the ELN", Santos said in a televised address.