Ruiz struck in the fifth and 14th minutes to get Junior off to a dynamic start before Huila's Cesar Hinestroza earned a goal back from the spot on 62 minutes.
But Junior held on to claim the three points and are two points clear of Deportivo Cali on top of the table.
Elswehere, dominant performances from strikers Wilson Morelo and Miguel Borja propelled La Equidad to a 5-2 thumping of Boyaca Chico.
In gaining a 4-1 lead at half-time, La Equidad's leading men both scored braces after Juan Perez opened the scoring for Chico.
Morelo completed a hat-trick and scored Equidad's fifth on 55 minutes before Cristian Alessandrini picked up a consolation strike for Chico in the 64th minute.
Millonarios had no problems accounting for Deportivo Pasto, winning 4-0 in front of their home fans.
Dayro Moreno scored a double either side of half-time before a penalty to Erick Moreno and late-strike to Wason Renteria completed the rout.
Itagui won their second game in a row as the defeated Deportes Quindio 2-0 with goals in each half.
In other results, Deportes Tolima overcame Cucuta Deportivo 2-1 while Deportivo Cali won 2-0 against Santa Fe.
Medellin lost 2-1 at home versus Once Caldas and Envigado played out a goalless draw with Alianza Petrolera.