Wislintos Renteria struck in second-half stoppage time for El Vigia after Aragua had looked certain to claim a draw thanks to Jaime Bustamante's 89th-minute equaliser.
The win made it eight points in four league matches for El Vigia, who lost six of their opening seven games in the Primera Division.
El Vigia moved up to 13th with 11 points and have a healthy gap over bottom side Yaracuyanos (four points).
With 15 minutes remaining at Aragua's Estadio Olimpico Hermanos Ghersi Paez the score remained 0-0 but in the 77th minute Darwin Gomez struck for the visitors.
Bustamante had seemingly secured a point for the home side when he scored 12 minutes later but in the first minute of stoppage time, Renteria found the back of the net for El Vigia, who are unbeaten in four league matches.
Deportivo Petare also continued their drive up the standings with a 2-1 triumph over Llaneros de Guanare, while Yaracuyanos, who prop up the 18-team league, lost their sixth consecutive game with a 5-2 defeat away to Trujillanos.
Deportivo Anzoategui remain top of the pile in Venezuela after a 2-1 win away to Deportivo La Guaira.
The victory took Anzoategui to 25 points after 11 games, one point ahead of second-placed Caracas, who defeated Tucanes 2-0.
Carabobo trumped Deportivo Lara 3-2, Atletico Venezuela edged out Zulia 1-0 and Mineros de Guayana defeated Deportivo Tachira by the same scoreline, while Estudiantes de Merida and Zamora's fixture was postponed.
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