"Sadly, we couldn't achieve our main goal to classify for the World Cup in Brazil," the 40-year-old Venezuelan said, announcing his resignation in an open letter to fans.
"That hurts us deeply because if we had achieved that we'd have given enormous joy to a nation submerged in a complex and difficult social and political situation."
Known as the 'Vinotinto' ('Red Wine') due to their burgundy-colored kit, Venezuela started fairly well in the South American qualifiers, fuelling hopes of a first World Cup appearance.
That dream provided welcome distraction from the nation's acrimonious political split between supporters and opponents of late socialist leader Hugo Chavez.
But Venezuela's chances faded in the final stages of the qualifying campaign, particularly after a home defeat by Uruguay, and Farias' departure was seen as inevitable.
A former defender in the local league before he entered management, Farias took over the national team at the end of 2007 and led them to the semi-finals of the 2011 Copa America tournament in Venezuelan soccer's greatest achievement.
His team also famously beat Argentina in their second match of the World Cup qualifiers two years ago although they could only finish in sixth place, five points behind Uruguay who reached the finals via an intercontinental playoff.
"The Vintotinto has made me proud," Farias said. "I wish to thank especially the players who, for six years, from the captains to the least experienced ones, sweated for the shirt."
Local media have speculated that Farias is now considering an offer to manage Mexican team Tijuana. He was due to speak at a news conference in Caracas on Monday.
(Additional reporting by Diego Ore; editing by Ken Ferris)
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