After Tolima beat Pereira on Saturday, Medellin also needed a win in order to reconquer the first place.
But David Castro put La Equidad ahead after less than two minutes and although his goal was cancelled out by Tressor Moreno seven minutes later, it was the home side that scored a 90th-minute winner through Ivan Corredor.
Real Cartagena failed to move into the top four as they lost 4-2 at Atletico Nacional.
Giovanni Moreno scored three of Nacional’s goals but was sent off with a second yellow card shortly after completing his hat-trick. The remaining home goal came from Jairo Palomino. Jose Najera and Edwards Jimenez hit the target for Cartagena.
In other matches on Sunday, Deportivo Cali beat Cortulua 5-3, Millonarios won 2-1 in a home match with Envigado, America de Cali suffered a 2-0 defeat at last-placed Quindio and Atletico Huila earned a 2-3 win at Cucuta.
Based on the current standings, Tolima, Medellin, Junior and Santa Fe are on course for a spot in the semi-finals.