Tolima hosted troubled Millonarios in Ibague and scored the opener through Rodrigo Marangoni in the 28th minute.
Yovanny Arrechea equalised 11 minutes later but Wilder Medina restored Tolima’s lead in the 73rd.
Millonarios finished two men down as Jose Mera and Arrechea were sent off late on.
Santa Fe surprisingly lost their home match against Chico 2-3 with all goals scored in the final half hour.
Antonhy Tapia broke the deadlock for the guests in the 64th but had his goal cancelled out by Mario Gonzalez a minute later.
But Chico remained focused and restored their lead through Diego Chica in the 71st, after which Tapia converted a penalty to set the score to 1-3. A late goal from Luis Yanes did nothing to avoid defeat for the home sides.
However, Santa Fe remain in third place as Junior lost 1-0 to Cartagena in Sunday’s coastal derby. The winning goal came from Nestor Salazar, from the penalty spot in the 84th minute.