Joao Osorio scored a late winner at the Estadio Jose Alberto Perez as Horacio Matuszyczk's men moved above Deportivo La Guaira.
James Cabezas had given the hosts the first-half lead, only for Miguel Mea Vitali to level for Caracas.
But Osorio's late goal was enough for Trujillanos, who are two points clear at the top thanks to the win.
Cabezas' eighth league goal of the campaign set up Trujillanos, but they gave up the lead in the 67th minute.
Osorio's first goal for Trujillanos came at the perfect time – in the third minute of additional time as he sent his team to the summit.