Libertad's bid to level leaders Olimpia on points was halted at 3 de Febrero in Wednesday's Paraguayan Division Profesional action.
The hosts in Ciudad del Este were 2-0 winners courtesy of a second-half brace from David Mendieta.
Raul Vicente Amarilla's men have now won back-to-back matches for the first time in almost 12 months, taking them seventh in the standings with 11 points.
Libertad, meanwhile, sit on 16 points, three shy of leaders Olimpia.
Nacional Asuncion are fourth, goal difference behind the third-placed Libertad, after a 2-1 home victory over Sportivo Luqueno.
Fredy Bareiro and Julio Santa Cruz had the capital club two goals clear at the interval, and despite conceding shortly after the break when Luis Mino struck, Asuncion held on for their fifth win in nine.