The victory saw Francisco Arce's men finish the second phase of the season unbeaten - with 14 wins and eight draws from 22 matches.
Daniel Guiza scored a brace for Cerro Porteno, while Angel Romero and Jose Ortigoza were also on target as they saw the club to 50 points in the Clausura phase.
Libertad pipped Deportivo Capiata for second spot, as the former won 1-0 away at Sol de America, while Capiata fell to a 3-2 loss at Rubio Nu.
Hugo Santacruz struck late for Libertad, with his 81st-minute goal taking the club to 39 points - one ahead of Capiata.
Rubio Nu held off Capiata, with goals to Matias Perez, Gustavo Viera and Gumersindo Mendieta helping them to their sixth win of the season and eighth spot.
Guarani could not move out of fourth position but finished the year with a flurry - thrashing cellar-dwellers Cerro Porteno PF 6-0.
Derlis Gonzalez struck a 14-minute hat-trick for Guarani, to take his season tally to nine goals.
Golden boot winner Rodrigo Lopez scored his 17th goal on the final day of the season, to help Sportivo Luqueno to a 1-1 draw away at Olimpia.
Lopez struck in the fifth minute, scoring the first goal in a game for the 10th time in the Clausura phase.
General Diaz finished in fifth spot, capitalising on Asuncion's loss to the champions with a 1-0 home win over Deportivo Carapegua.
