After watching Libertad clinch the Paraguay's top-flight Apertura title last week, Benitez and Fernandez scored two goals apiece to ensure second-placed Guarani ended the campaign on a winning note at the Estadio Defensores del Chaco on Thursday.
With Libertad claiming a narrow 1-0 win over Olimpia on Saturday, the result against Nacional saw Guarani finish four points behind the recently crowned champions after 22 rounds.
Fernando Jubero's men had gone nine games unbeaten heading into the match and that streak never threatened to end thanks to Benitez, who opened the scoring in the 34th minute.
Fernandez doubled the visitors' advantage nine minutes into the second half before Jorge Mendoza got himself on the scoresheet eight minutes later.
Benitez netted his second of the game in the 69th minute - taking his tally to 11 goals from his past 10 games, a run that included three braces.
Sandino Sosa pulled a goal back for Nacional, finding the back of the net three minutes later but Guarani quickly restored their four-goal advantage through Fernandez, who made it nine goals in seven games with his 77th-minute effort.
The home side were on target again courtesy of Enrique Araujo's 79th-minute penalty, though Guarani had the final say as defender Julio Caceres stepped up to convert another spot-kick with two minutes remaining.
On Saturday, Rodrigo Lopez's 82nd-minute goal was all that separated Libertad and third-placed Olimpia at the Estadio Dr Nicolas Leoz.
In other results over the weekend, Cerro Porteno finished the campaign in fourth position after Sol de America and Rubio Nu both slipped up.
Former Spain international Daniel Guiza scored twice to inspire Cerro Porteno to a 2-1 win at home to General Diaz on Friday.
The result ensured Cerro Porteno (31 points, +11) finished ahead of Sol de America on goal difference (31 points, +5) after they played out a goalless draw with Sportivo Luqueno on Friday.
Cerro Porteno were a point clear of Rubio Nu, who drew 1-1 at cellar-dwellers 3 de Febrero on Saturday.
Meanwhile, Deportivo Capiata accounted for second-bottom 12 de Octubre 2-0 on Friday.
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