Mr. Santos’s opponents in the Congress were furious the new accord had been pushed through with what they said was too little time to either comment or review the changes. The president, who has staked his legacy on ending the long conflict with the rebel group, the Revolutionary Armed Forces of Colombia, or FARC, consulted his opponents shortly after the referendum was defeated, but he has largely kept them in the dark since, they said.

The Congress’s vote brings to a close what had become one of the country’s biggest political dramas in decades.

After years of tense talks in Havana, rebel and government negotiators announced in August they had reached a deal to end a half century of war which left more than 200,000 people dead. The next month, the rebels arrived to the port city of Cartagena, where a celebratory signing was held before world leaders and televised to the nation.

Just one piece remained: A popular vote to approve the accord, which polls had shown would be a shoo-in. Instead, it lost by a narrow margin. Then days later, in another twist, Mr. Santos was awarded the Nobel Peace Prize. In their announcement of the prize, the Norwegian judges acknowledged the referendum’s defeat but said they hoped that the prize would “give him strength to succeed in this demanding task.”

Though most voters supported peace with the rebels, many, noting the FARC’s long history of kidnappings and killings, felt the deal offered too much leniency, including reduced sentences in exchange for confessions. Yet Mr. Santos also faced a challenge in renegotiating new terms with the rebels, who had been promised new lives as civilians and a clean slate.