Fernando Uribe and Wilder Guisao scored just either side of half-time to give Nacional a two-goal lead in front of their home crowd and although Quindio struck in the 59th minute through goalkeeper Julian Viafara, the hosts held on for their fifth straight league victory.
Nacional are top of the Primera A standings, four points clear of Millonarios, who were denied victory when Boyaca Chico struck in second-half injury time to claim a 1-1 draw.
It was 2-0 in the 54th minute when Guisao got on the end of a counter-attack, cut inside his defender and lifted his shot over Viafara but Quindio's goalkeeper gave the visitors some hope five minutes later when he curled a free-kick into the net.
Despite Viafara's first goal since 2011, Quindio could not manage an equaliser and Nacional held on for victory.
In Tunja, Millonarios looked on track for their fifth consecutive league win after Harrison Otalvaro's 67th-minute goal but a penalty in second-half stoppage time from Edwin Movil ensured Boyaca Chico claimed a point at home.
