In a 30-minute video posted on the Internet, Timoleon Jimenez, alias "Timochenko," warned that the FARC "will do what's necessary if the oligarchy persists in blocking peace."
The video celebrating the Marxist rebels' 50 years comes amid intensifying debate in Colombia over the peace talks with the government, which are taking place in Havana.
Santos, who has staked his political future on the bid to end Latin America's longest insurgency, came in second over the weekend in the first round of presidential elections to a vehement opponent of the talks, Oscar Ivan Zuluaga. The vote goes to a runoff on June 15.
"What I want is to finish this process as soon as possible to put an end to the war," he said in an interview with W radio.
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Despite partial agreement on certain issues like the FARC's return to political life, a comprehensive peace has so far eluded negotiators.
"We are in Havana because we dream of an effective peace," the FARC chief said.
But he struck a defiant tone in his videotaped message, which was reprinted in its entirety on the FARC's website (www.Farc-ep.Co).
Timochenko noted that while Santos accuses the opposition of seeking to "assassinate the Colombian peoples' hopes for peace," the Colombian president has rejected repeated rebel calls for a ceasefire.
"As if every day he weren't ordering the intensification of military operations and bombings in its eagerness to kill the leaders of the insurgency with which he is holding a dialogue with in Havana," he said of Santos.
"National reconciliation must pass through the dismantling of political hatreds and annihilation implemented from the highest positions of the state," he said.