With Cerro Porteno's goalless draw against Olimpia, three points for Capiata would have seen the deficit reduced to seven points.
But Libertad had other ideas as they went ahead through Jorge Moreira in the sixth minute and Miguel Samudio doubled the advantage on 25 minutes.
Captiata rallied late and mounted a fight-back after Cristian Lopez's 71st-minute goal but ultimately could not force their way back into the match.
Nacional Asuncion extended their unbeaten run to five games after a flurry of second-half goals secured a 4-1 win at Deportivo Carapegua.
Derlis Gonzalez scored a double as Guarani trounced Sportivo Luqueno 4-0 on the road.
In other matches, General Diaz drew 2-2 with Rubio Nu and Cerro Porteno PF won 3-0 against Sol de America.
