Pumas took an early 1-0 lead in the 17th minute at the Estadio Olimpico Universitario. Francisco Palencia's touch went off Toronto defender Andy Iro and right to Bravo, who only had goalkeeper Milos Kocic to beat. Kocic came out to play the ball, but Bravo struck it past the 'keeper.
Pumas made it 2-0 in the 21st minute. Bravo finished a dangerous run into the Toronto box by sending a pass by Iro to trailing defender Efrain Velarde, who had no problem beating a helpless Kocic.
Bravo's second goal of the game in the 33rd minute made it 3-0. Bravo outran Toronto defender Ty Hardin to catch up to a long ball, then fired a left-footed strike that Kocic couldn't handle.
Bravo completed the hat trick in the 42nd minute as he broke free of the Toronto defence onside and caught up to a long feed from Palencia, then fired the ball off the left post and into the Toronto goal.
Pumas continued to carry the play in the second half, but Kocic made a pair of big saves in the 65th minute to prevent the game spinning further out of his team's grasp.
In Wednesday's other Group C match, FC Dallas tied Tauro 1-1. Dallas leads the group with seven points, followed by Pumas with four, Toronto with three and Tauro with two. The top two teams from the group advance to the quarter-finals.
Toronto won its group stage opener 2-1 at Tauro in Panama City before losing 1-0 to visiting FC Dallas in a game that stretched over two days due to bad weather.
Pumas lost its opener 1-0 at home to FC Dallas before tying Tauro 0-0 in Panama.
Winless in five games in the Mexican Apertura, Pumas are in a four-way tie for sixth in the domestic standings. Traditionally the Mexican side uses the CONCACAf Champions League to give its young players experience.
Toronto (5-12-12) stands last in the MLS Eastern Conference but is coming off its first away league win of the season -- 4-2 over Columbus.
That win cost Toronto the services of forward Joao Plata, who has a strained hamstring. Midfielder Matt Stinson was cleared to play despite a foot injury but doctors balked at him flying.
Defender Richard Eckersley was suspended and midfielder Eric Avila cup-tied after appearing in the competition for Dallas.
Goalkeeper Stefan Frei made the trip despite leaving the Columbus game with a charley-horse, but Kocic continued his trend of starting Champions League games.