It is the first time Pumas have reached the title playoffs since 2011 when they won the Clausura championship with Cortes in their side.
The top eight after the 17-match league phase go into two-legged quarter-finals and one berth remains up for grabs next weekend.
Pumas climbed into seventh place in the standings with 26 points from 16 matches. They are six points behind leaders America, UANL Tigres and Atlas with Santos Laguna (29), Morelia (27) and Cruz Azul (26) also qualified.
The striker, who took his tally to six, scored at either end of the match with a volley in the eighth minute and a header in the 89th. Paraguayan Robin Ramirez scored Pumas' second on the stroke of halftime.
Tigres, beaten 1-0 at home by Monterrey on Saturday, were knocked off top place for the first time since January.
America went top on goal difference when they recovered from two goals down to win 4-2 at Pachuca, scoring four goals in 16 minutes including a hat-trick by Ecuador striker Cristian Benitez that put him top of the scorers list with 12.
"This is the America I want to see, we showed that when the team step on the accelerator they overrun their rivals," coach Miguel Herrera told reporters.
"I see a very strong team, solid and united. You make history with trophies in your cabinet and I'm convinced this team is built for that."
Cruz Azul notched their fourth consecutive victory, 1-0 at home to Santos Laguna with a 35th-minute goal headed by Argentine midfielder Christian Gimenez at a corner, and secured their quarter-final place.
Title holders Tijuana, winners of the Apertura championship in the first half of the season, lost 1-0 at lowly San Luis, conceding an 86th-minute goal to Alan Zamora after having two players sent off early in the second half.
The team from the Baja California border town, who won their first title in December, have suffered from a dramatic slump domestically while qualifying for the knockout phase in South America's elite Libertadores Cup club tournament.
Tijuana meet Brazil's Palmeiras in the last 16 with the first leg at their Caliente ground on Tuesday.
Morelia bagged their place in the top eight with a 2-1 home win over Toluca on Friday.
Guadalajara, whose hopes of qualifying ended with Monterrey's win over Tigres, have been struggling since 2011 with coach Benjamin Galindo unable to turn things round after the failure of a year-long experiment under the consultancy of Dutch great Johan Cruyff.
The Chivas reached the Apertura playoffs at the end of last year but were knocked out in the quarter-finals, Cruyff and Dutch coach John van't Schip were sacked and Galindo took charge.
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