Milton Maygua's men climbed to ninth in the Bolivian top flight, and denied Club Universitario a victory that would have taken them to fourth.
Diego Rivero opened the scoring in Yacuiba, netting in the 14th minute before Juan Rios levelled for the hosts eight minutes prior to the interval.
Colombian forward Jeison Quinones was the difference, his goal in the 75th minute continuing Yacuiba's form and ending Club Universitario's three-game winning streak.
It was a poor loss for Universitario, considering they will next face top-two sides Bolivar and Oriente Petrolero to finish November.
Yacuiba, meanwhile, will look to continue their winning run when they travel to face Nacional Potosi, the team they went three points clear of on Sunday.
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