Medellin replaced Deportivo Cali at the summit after their victory as the former leaders lost at Patriotas Boyaca.
Hernan Torres' side eventually saw off Uniautonoma on Wednesday thanks to Andres Mosquera's 68th-minute goal.
The defender had not scored since September last year but his effort proved crucial for the new table-toppers.
Cali - who overtook Once Caldas in the league lead last week - quickly relinquished their advantage with a 1-0 loss in Tunja on Thursday.
Jonathan Estrada Campilo scored the only goal of the game in the 34th minute for Patriotas.
Cali have now dropped to fourth - Santa Fe and Caldas overtaking them.
Santa Fe cruised to a 2-0 win over rock-bottom La Equidad while Caldas were emphatic in a 4-1 triumph against Boyaca Chico.
Scores were locked at 1-1 before Gustavo Culma's goal on the stroke of half-time changed the complexion of the match.
Jaime Ramirez and Cristian Palomeque added goals in the last 15 minutes for Caldas.
Fortaleza moved four points away from the foot of the table after Jhonathan Caicedo Vergara's 86th-minute strike gave them a 2-1 home win over Alianza Petrolera.
Aguilas Pereira snapped a run of three straight losses with a 4-2 win over Millonarios.
Elsewhere, Junior edged Deportes Tolima 1-0 and Atletico Huila and Envigado played out a 1-1 draw.
